{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.platform = \"BGISEQ\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[28093, "SRR26196850", "SRX21908248", "SRS18993956", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 4", "GSM7808262", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 4", "Standard processing by BGI.p HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808262", "GSM7808262: elipsa mutant  clutch 4; Danio rerio; RNA Seq", "GSM7808262 r1", "GSM7808262", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT4_1.fq.gz ElipsaMUT4_2.fq.gz", "fastq fastq", 4536153000.0, 22680765.0, "GSM7808262 r1", "0:100 1:100", "A:1194964224;C:1059904764;G:1074108947;T:1207175065;N:0", 100, 100, null, null, 1194964224, 1059904764, 1074108947, 1207175065, 0, "SRX21908248", "SRS18993956", "SRA1721841", "NTNU", "NTNU", 2, 0.93991, 0.94735, 0.10392, 0.10318, 0.66434, 0.66344, 0.48911, 0.49311, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28094, "SRR26196851", "SRX21908247", "SRS18993955", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 3", "GSM7808261", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 3", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808261", "GSM7808261: elipsa mutant  clutch 3; Danio rerio; RNA Seq", "GSM7808261 r1", "GSM7808261", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT3_1.fq.gz ElipsaMUT3_2.fq.gz", "fastq fastq", 4547581600.0, 22737908.0, "GSM7808261 r1", "0:100 1:100", "A:1183476304;C:1077021222;G:1092963681;T:1194120393;N:0", 100, 100, null, null, 1183476304, 1077021222, 1092963681, 1194120393, 0, "SRX21908247", "SRS18993955", "SRA1721841", "NTNU", "NTNU", 2, 0.95029, 0.95874, 0.09085, 0.09059, 0.66856, 0.66722, 0.48534, 0.48545, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28095, "SRR26196852", "SRX21908246", "SRS18993954", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 2", "GSM7808260", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 2", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808260", "GSM7808260: elipsa mutant  clutch 2; Danio rerio; RNA Seq", "GSM7808260 r1", "GSM7808260", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT2_1.fq.gz ElipsaMUT2_2.fq.gz", "fastq fastq", 4544444600.0, 22722223.0, "GSM7808260 r1", "0:100 1:100", "A:1186329827;C:1072965608;G:1087757513;T:1197391652;N:0", 100, 100, null, null, 1186329827, 1072965608, 1087757513, 1197391652, 0, "SRX21908246", "SRS18993954", "SRA1721841", "NTNU", "NTNU", 2, 0.94545, 0.95403, 0.09705, 0.09653, 0.66576, 0.66466, 0.47893, 0.47882, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28096, "SRR26196853", "SRX21908245", "SRS18993953", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 1", "GSM7808259", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 1", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808259", "GSM7808259: elipsa mutant  clutch 1; Danio rerio; RNA Seq", "GSM7808259 r1", "GSM7808259", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT1_1.fq.gz ElipsaMUT1_2.fq.gz", "fastq fastq", 4561346400.0, 22806732.0, "GSM7808259 r1", "0:100 1:100", "A:1192227498;C:1073309826;G:1091718946;T:1204090130;N:0", 100, 100, null, null, 1192227498, 1073309826, 1091718946, 1204090130, 0, "SRX21908245", "SRS18993953", "SRA1721841", "NTNU", "NTNU", 2, 0.94079, 0.94928, 0.09838, 0.09859, 0.67093, 0.66975, 0.47837, 0.4824, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28097, "SRR26196854", "SRX21908244", "SRS18993950", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 4", "GSM7808258", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 4", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808258", "GSM7808258: elipsa control  clutch 4; Danio rerio; RNA Seq", "GSM7808258 r1", "GSM7808258", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL4_1.fq.gz ElipsaCTRL4_2.fq.gz", "fastq fastq", 4534543600.0, 22672718.0, "GSM7808258 r1", "0:100 1:100", "A:1195456125;C:1060510332;G:1073683545;T:1204893598;N:0", 100, 100, null, null, 1195456125, 1060510332, 1073683545, 1204893598, 0, "SRX21908244", "SRS18993950", "SRA1721841", "NTNU", "NTNU", 2, 0.94686, 0.95523, 0.0948, 0.09459, 0.66259, 0.66093, 0.49251, 0.49154, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28098, "SRR26196855", "SRX21908243", "SRS18993952", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 3", "GSM7808257", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 3", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808257", "GSM7808257: elipsa control  clutch 3; Danio rerio; RNA Seq", "GSM7808257 r1", "GSM7808257", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL3_1.fq.gz ElipsaCTRL3_2.fq.gz", "fastq fastq", 4546464800.0, 22732324.0, "GSM7808257 r1", "0:100 1:100", "A:1192169234;C:1070218166;G:1081895902;T:1202181498;N:0", 100, 100, null, null, 1192169234, 1070218166, 1081895902, 1202181498, 0, "SRX21908243", "SRS18993952", "SRA1721841", "NTNU", "NTNU", 2, 0.94937, 0.95815, 0.09867, 0.09825, 0.66574, 0.66478, 0.49056, 0.48959, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28099, "SRR26196856", "SRX21908242", "SRS18993951", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 2", "GSM7808256", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 2", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808256", "GSM7808256: elipsa control  clutch 2; Danio rerio; RNA Seq", "GSM7808256 r1", "GSM7808256", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL2_1.fq.gz ElipsaCTRL2_2.fq.gz", "fastq fastq", 4557679200.0, 22788396.0, "GSM7808256 r1", "0:100 1:100", "A:1184954651;C:1080955864;G:1098377272;T:1193391413;N:0", 100, 100, null, null, 1184954651, 1080955864, 1098377272, 1193391413, 0, "SRX21908242", "SRS18993951", "SRA1721841", "NTNU", "NTNU", 2, 0.94378, 0.95076, 0.0855, 0.0847, 0.66604, 0.66342, 0.48858, 0.48404, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28100, "SRR26196857", "SRX21908241", "SRS18993949", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 1", "GSM7808255", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 1", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808255", "GSM7808255: elipsa control  clutch 1; Danio rerio; RNA Seq", "GSM7808255 r1", "GSM7808255", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL1_1.fq.gz ElipsaCTRL1_2.fq.gz", "fastq fastq", 4566618600.0, 22833093.0, "GSM7808255 r1", "0:100 1:100", "A:1193092402;C:1076659586;G:1094193492;T:1202673120;N:0", 100, 100, null, null, 1193092402, 1076659586, 1094193492, 1202673120, 0, "SRX21908241", "SRS18993949", "SRA1721841", "NTNU", "NTNU", 2, 0.94269, 0.94899, 0.09816, 0.09712, 0.66991, 0.66925, 0.47671, 0.46995, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30075, "SRR27700027", "SRX23366859", "SRS20229171", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 4", "GSM8031712", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 4", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031712", "GSM8031712: Smh mutant  clutch 4; Danio rerio; RNA Seq", "GSM8031712 r1", "GSM8031712", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT4_1.fq.gz SmhMUT4_2.fq.gz", "fastq fastq", 4550057400.0, 22750287.0, "GSM8031712 r1", "0:100 1:100", "A:1198976754;C:1064190197;G:1077491671;T:1209398778;N:0", 100, 100, null, null, 1198976754, 1064190197, 1077491671, 1209398778, 0, "SRX23366859", "SRS20229171", "SRA1790727", "NTNU", "NTNU", 2, 0.94285, 0.95266, 0.101, 0.10096, 0.66145, 0.65989, 0.48209, 0.47768, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30076, "SRR27700028", "SRX23366858", "SRS20229175", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 3", "GSM8031711", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 3", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031711", "GSM8031711: Smh mutant  clutch 3; Danio rerio; RNA Seq", "GSM8031711 r1", "GSM8031711", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT3_1.fq.gz SmhMUT3_2.fq.gz", "fastq fastq", 4545452600.0, 22727263.0, "GSM8031711 r1", "0:100 1:100", "A:1188958937;C:1071903723;G:1087032258;T:1197557682;N:0", 100, 100, null, null, 1188958937, 1071903723, 1087032258, 1197557682, 0, "SRX23366858", "SRS20229175", "SRA1790727", "NTNU", "NTNU", 2, 0.94501, 0.95409, 0.09005, 0.08947, 0.66149, 0.66062, 0.46824, 0.48019, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30077, "SRR27700029", "SRX23366857", "SRS20229173", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 2", "GSM8031710", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 2", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031710", "GSM8031710: Smh mutant  clutch 2; Danio rerio; RNA Seq", "GSM8031710 r1", "GSM8031710", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT2_1.fq.gz SmhMUT2_2.fq.gz", "fastq fastq", 4548042000.0, 22740210.0, "GSM8031710 r1", "0:100 1:100", "A:1184618587;C:1077947166;G:1089628929;T:1195847318;N:0", 100, 100, null, null, 1184618587, 1077947166, 1089628929, 1195847318, 0, "SRX23366857", "SRS20229173", "SRA1790727", "NTNU", "NTNU", 2, 0.94502, 0.95416, 0.09209, 0.092, 0.66407, 0.66214, 0.48538, 0.48509, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30078, "SRR27700030", "SRX23366856", "SRS20229174", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 1", "GSM8031709", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 1", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031709", "GSM8031709: Smh mutant  clutch 1; Danio rerio; RNA Seq", "GSM8031709 r1", "GSM8031709", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT1_1.fq.gz SmhMUT1_2.fq.gz", "fastq fastq", 4544759600.0, 22723798.0, "GSM8031709 r1", "0:100 1:100", "A:1194011331;C:1066502346;G:1077923006;T:1206322917;N:0", 100, 100, null, null, 1194011331, 1066502346, 1077923006, 1206322917, 0, "SRX23366856", "SRS20229174", "SRA1790727", "NTNU", "NTNU", 2, 0.945, 0.95433, 0.09733, 0.09796, 0.66034, 0.65951, 0.477, 0.47705, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30079, "SRR27700031", "SRX23366855", "SRS20229172", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 4", "GSM8031708", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 4", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031708", "GSM8031708: Smh control  clutch 4; Danio rerio; RNA Seq", "GSM8031708 r1", "GSM8031708", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz", "fastq fastq", 4536141000.0, 22680705.0, "GSM8031708 r1", "0:100 1:100", "A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0", 100, 100, null, null, 1196842043, 1059535727, 1071488375, 1208274855, 0, "SRX23366855", "SRS20229172", "SRA1790727", "NTNU", "NTNU", 2, 0.94102, 0.95093, 0.09453, 0.09431, 0.66403, 0.6631, 0.49804, 0.49818, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30080, "SRR27700032", "SRX23366854", "SRS20229170", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 3", "GSM8031707", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 3", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031707", "GSM8031707: Smh control  clutch 3; Danio rerio; RNA Seq", "GSM8031707 r1", "GSM8031707", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL3_1.fq.gz SmhCTRL3_2.fq.gz", "fastq fastq", 4543416000.0, 22717080.0, "GSM8031707 r1", "0:100 1:100", "A:1189755812;C:1071666785;G:1082665579;T:1199327824;N:0", 100, 100, null, null, 1189755812, 1071666785, 1082665579, 1199327824, 0, "SRX23366854", "SRS20229170", "SRA1790727", "NTNU", "NTNU", 2, 0.94571, 0.95506, 0.08989, 0.09005, 0.6632, 0.66107, 0.49631, 0.49649, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30081, "SRR27700033", "SRX23366853", "SRS20229169", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 2", "GSM8031706", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 2", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031706", "GSM8031706: Smh control  clutch 2; Danio rerio; RNA Seq", "GSM8031706 r1", "GSM8031706", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL2_2.fq.gz SmhCTRL2_1.fq.gz", "fastq fastq", 4536576000.0, 22682880.0, "GSM8031706 r1", "0:100 1:100", "A:1180961957;C:1074391564;G:1088552770;T:1192669709;N:0", 100, 100, null, null, 1180961957, 1074391564, 1088552770, 1192669709, 0, "SRX23366853", "SRS20229169", "SRA1790727", "NTNU", "NTNU", 2, 0.94324, 0.95313, 0.08618, 0.08685, 0.66399, 0.66216, 0.49362, 0.49644, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30082, "SRR27700034", "SRX23366852", "SRS20229168", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 1", "GSM8031705", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 1", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031705", "GSM8031705: Smh control  clutch 1; Danio rerio; RNA Seq", "GSM8031705 r1", "GSM8031705", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL1_1.fq.gz SmhCTRL1_2.fq.gz", "fastq fastq", 4546026800.0, 22730134.0, "GSM8031705 r1", "0:100 1:100", "A:1201447089;C:1060722844;G:1073012718;T:1210844149;N:0", 100, 100, null, null, 1201447089, 1060722844, 1073012718, 1210844149, 0, "SRX23366852", "SRS20229168", "SRA1790727", "NTNU", "NTNU", 2, 0.94554, 0.95419, 0.09192, 0.09168, 0.66436, 0.66222, 0.4762, 0.48114, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34182, "SRR31399561", "SRX26768859", "SRS23256160", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "eif6 3", "GSM8641203", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing", "eif6 3", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO", "GSM8641203", "GSM8641203: eif6 3; Danio rerio; RNA Seq", "GSM8641203 r1", "GSM8641203", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "eif6_3_1.fq.gz eif6_3_2.fq.gz", "fastq fastq", 6955801200.0, 34779006.0, "GSM8641203 r1", "0:100 1:100", "A:1784502248;C:1653592398;G:1716091635;T:1801614919;N:0", 100, 100, null, null, 1784502248, 1653592398, 1716091635, 1801614919, 0, "SRX26768859", "SRS23256160", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34183, "SRR31399562", "SRX26768858", "SRS23256161", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "eif6 2", "GSM8641202", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing", "eif6 2", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO", "GSM8641202", "GSM8641202: eif6 2; Danio rerio; RNA Seq", "GSM8641202 r1", "GSM8641202", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "eif6_2_1.fq.gz eif6_2_2.fq.gz", "fastq fastq", 6968721400.0, 34843607.0, "GSM8641202 r1", "0:100 1:100", "A:1798630009;C:1650901437;G:1708195694;T:1810994260;N:0", 100, 100, null, null, 1798630009, 1650901437, 1708195694, 1810994260, 0, "SRX26768858", "SRS23256161", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34184, "SRR31399563", "SRX26768857", "SRS23256159", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "eif6 1", "GSM8641201", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing", "eif6 1", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO", "GSM8641201", "GSM8641201: eif6 1; Danio rerio; RNA Seq", "GSM8641201 r1", "GSM8641201", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "eif6_1_1.fq.gz eif6_1_2.fq.gz", "fastq fastq", 6976474200.0, 34882371.0, "GSM8641201 r1", "0:100 1:100", "A:1819387431;C:1630709320;G:1698463303;T:1827914146;N:0", 100, 100, null, null, 1819387431, 1630709320, 1698463303, 1827914146, 0, "SRX26768857", "SRS23256159", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34185, "SRR31399564", "SRX26768856", "SRS23256158", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "wt3", "GSM8641200", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing", "wt3", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype", "GSM8641200", "GSM8641200: wt3; Danio rerio; RNA Seq", "GSM8641200 r1", "GSM8641200", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "wt3_1.fq.gz wt3_2.fq.gz", "fastq fastq", 6990771600.0, 34953858.0, "GSM8641200 r1", "0:100 1:100", "A:1823561732;C:1639273273;G:1691098287;T:1836838308;N:0", 100, 100, null, null, 1823561732, 1639273273, 1691098287, 1836838308, 0, "SRX26768856", "SRS23256158", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34186, "SRR31399565", "SRX26768855", "SRS23256157", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "wt2", "GSM8641199", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing", "wt2", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype", "GSM8641199", "GSM8641199: wt2; Danio rerio; RNA Seq", "GSM8641199 r1", "GSM8641199", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "wt2_1.fq.gz wt2_2.fq.gz", "fastq fastq", 6996780600.0, 34983903.0, "GSM8641199 r1", "0:100 1:100", "A:1819793027;C:1646550105;G:1701161650;T:1829275818;N:0", 100, 100, null, null, 1819793027, 1646550105, 1701161650, 1829275818, 0, "SRX26768855", "SRS23256157", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34187, "SRR31399566", "SRX26768854", "SRS23256156", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "wt1", "GSM8641198", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing", "wt1", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype", "GSM8641198", "GSM8641198: wt1; Danio rerio; RNA Seq", "GSM8641198 r1", "GSM8641198", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "wt1_1.fq.gz wt1_2.fq.gz", "fastq fastq", 6976844600.0, 34884223.0, "GSM8641198 r1", "0:100 1:100", "A:1807619362;C:1649374675;G:1693243894;T:1826606669;N:0", 100, 100, null, null, 1807619362, 1649374675, 1693243894, 1826606669, 0, "SRX26768854", "SRS23256156", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [50717, "SRR8257205", "SRX5074433", "SRS4088243", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 3", "GSM3494529", null, "tissue:whole embryo|developmental stage:36hpf|genotype:WT", "RNAseq in zebrafish wild type embryos at 36hpf replicate 3", "Reads were aligned against reference genome using STAR software  and reads per gene were counted 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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:WT", "GSM3494529", "GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq", "GSM3494529", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_WT_36hpf_rep3.fq.gz", "fastq", 2560587500.0, 51211750.0, "GSM3494529 r1", "0:50", "A:719232941;C:550474431;G:576590260;T:714289868;N:0", 50, null, null, null, 719232941, 550474431, 576590260, 714289868, 0, "SRX5074433", "SRS4088243", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93981, null, 0.10951, null, 0.71388, null, 0.48297, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50718, "SRR8257204", "SRX5074432", "SRS4088242", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 2", "GSM3494528", null, "tissue:whole embryo|developmental stage:36hpf|genotype:WT", "RNAseq in zebrafish wild type embryos at 36hpf replicate 2", "Reads were aligned against reference genome using STAR software  and reads per gene were counted 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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:WT", "GSM3494528", "GSM3494528: RNAseq in zebrafish wild type embryos at 36hpf replicate 2; Danio rerio; RNA Seq", "GSM3494528", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_WT_36hpf_rep2.fq.gz", "fastq", 2775840750.0, 55516815.0, "GSM3494528 r1", "0:50", "A:783053027;C:587947172;G:603351259;T:801489292;N:0", 50, null, null, null, 783053027, 587947172, 603351259, 801489292, 0, "SRX5074432", "SRS4088242", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93386, null, 0.11853, null, 0.7007, null, 0.48856, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50719, "SRR8257203", "SRX5074431", "SRS4088241", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 1", "GSM3494527", null, "tissue:whole embryo|developmental stage:36hpf|genotype:WT", "RNAseq in zebrafish wild type embryos at 36hpf replicate 1", "Reads were aligned against reference genome using STAR software  and reads per gene were counted 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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:WT", "GSM3494527", "GSM3494527: RNAseq in zebrafish wild type embryos at 36hpf replicate 1; Danio rerio; RNA Seq", "GSM3494527", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_WT_36hpf_rep1.fq.gz", "fastq", 2638769750.0, 52775395.0, "GSM3494527 r1", "0:50", "A:749627286;C:556213831;G:574654547;T:758274086;N:0", 50, null, null, null, 749627286, 556213831, 574654547, 758274086, 0, "SRX5074431", "SRS4088241", "SRA815839", "GEO", "CABD/CSIC", 1, 0.92992, null, 0.12022, null, 0.72174, null, 0.49097, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50720, "SRR8257202", "SRX5074430", "SRS4088240", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3", "GSM3494526", null, "tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ", "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3", "Reads were aligned against reference genome using STAR software  and reads per gene were counted 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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:tp63  / ", "GSM3494526", "GSM3494526: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3; Danio rerio; RNA Seq", "GSM3494526", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_p63mut_36hpf_rep3.fq.gz", "fastq", 2651169450.0, 53023389.0, "GSM3494526 r1", "0:50", "A:752539060;C:560162268;G:581624300;T:756843822;N:0", 50, null, null, null, 752539060, 560162268, 581624300, 756843822, 0, "SRX5074430", "SRS4088240", "SRA815839", "GEO", "CABD/CSIC", 1, 0.94022, null, 0.12949, null, 0.70019, null, 0.50336, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50721, "SRR8257201", "SRX5074429", "SRS4088239", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2", "GSM3494525", null, "tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ", "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2", "Reads were aligned against reference genome using STAR software  and reads per gene were counted 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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:tp63  / ", "GSM3494525", "GSM3494525: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2; Danio rerio; RNA Seq", "GSM3494525", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_p63mut_36hpf_rep2.fq.gz", "fastq", 2821501700.0, 56430034.0, "GSM3494525 r1", "0:50", "A:795357588;C:599294949;G:620563224;T:806285939;N:0", 50, null, null, null, 795357588, 599294949, 620563224, 806285939, 0, "SRX5074429", "SRS4088239", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93671, null, 0.12314, null, 0.6957, null, 0.48362, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50722, "SRR8257200", "SRX5074428", "SRS4088238", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1", "GSM3494524", null, "tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ", "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1", "Reads were aligned against reference genome using STAR software  and reads per gene were counted 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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:tp63  / ", "GSM3494524", "GSM3494524: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1; Danio rerio; RNA Seq", "GSM3494524", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_p63mut_36hpf_rep1.fq.gz", "fastq", 2592494100.0, 51849882.0, "GSM3494524 r1", "0:50", "A:730978948;C:550803197;G:572081489;T:738630466;N:0", 50, null, null, null, 730978948, 550803197, 572081489, 738630466, 0, "SRX5074428", "SRS4088238", "SRA815839", "GEO", "CABD/CSIC", 1, 0.94035, null, 0.11571, null, 0.70796, null, 0.49468, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [52242, "SRR9047069", "SRX5823596", "SRS4751717", "SRP198207", "PRJNA542583", "Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation", "PRJNA542583", "Other", "Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis.", null, null, null, "stdMO PBS", "stdMO PBS", null, "strain:Tu|isolate:primary cell|dev stage:gastrulation|sex:not determined|tissue:embryo|collection date:2016 11 13|genotype:wild type|geo loc name:China: Beijing|sample type:embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tspan RNA seq", "uniprot", "uniprot", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP198207", null, null, "161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz", "fastq", 633650654.0, 12931646.0, "161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz", "0:49 1:0", "A:165787428;C:152969494;G:145599180;T:169168973;N:125579", 49, 0, null, null, 165787428, 152969494, 145599180, 169168973, 125579, "SRX5823596", "SRS4751717", "SRA885639", "Tsinghua University|School of Life Sciences", "Tsinghua University", 1, 0.93004, null, 0.09559, null, 0.753, null, 0.47488, null, 49, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-30", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52944, "SRR9609439", "SRX6372833", "SRS5033898", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 3", "GSM3909672", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909672", "GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq", "GSM3909672", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909672", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1283013300.0, 25660266.0, "GSM3909672 r1", "0:50", "A:339417002;C:304649204;G:297783450;T:341163644;N:0", 50, null, null, null, 339417002, 304649204, 297783450, 341163644, 0, "SRX6372833", "SRS5033898", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94342, null, 0.10559, null, 0.72401, null, 0.47431, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52945, "SRR9609438", "SRX6372832", "SRS5033897", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 2", "GSM3909671", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909671", "GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq", "GSM3909671", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909671", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1282475700.0, 25649514.0, "GSM3909671 r1", "0:50", "A:339635626;C:302447093;G:295507893;T:344885088;N:0", 50, null, null, null, 339635626, 302447093, 295507893, 344885088, 0, "SRX6372832", "SRS5033897", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94396, null, 0.10502, null, 0.71465, null, 0.47566, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52946, "SRR9609437", "SRX6372831", "SRS5033896", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 1", "GSM3909670", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909670", "GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq", "GSM3909670", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909670", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1147572700.0, 22951454.0, "GSM3909670 r1", "0:50", "A:300633532;C:273711082;G:268229512;T:304998574;N:0", 50, null, null, null, 300633532, 273711082, 268229512, 304998574, 0, "SRX6372831", "SRS5033896", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94418, null, 0.09965, null, 0.72746, null, 0.47644, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52947, "SRR9609436", "SRX6372830", "SRS5033895", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 3", "GSM3909669", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909669", "GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq", "GSM3909669", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909669", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1282414400.0, 25648288.0, "GSM3909669 r1", "0:50", "A:334687310;C:307161534;G:302070174;T:338495382;N:0", 50, null, null, null, 334687310, 307161534, 302070174, 338495382, 0, "SRX6372830", "SRS5033895", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94359, null, 0.09476, null, 0.72529, null, 0.47117, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52948, "SRR9609435", "SRX6372829", "SRS5033894", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 2", "GSM3909668", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909668", "GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq", "GSM3909668", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909668", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1281370000.0, 25627400.0, "GSM3909668 r1", "0:50", "A:335735118;C:306450529;G:298815464;T:340368889;N:0", 50, null, null, null, 335735118, 306450529, 298815464, 340368889, 0, "SRX6372829", "SRS5033894", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94338, null, 0.09412, null, 0.7204, null, 0.48662, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52949, "SRR9609434", "SRX6372828", "SRS5033893", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 1", "GSM3909667", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909667", "GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq", "GSM3909667", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909667", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1278504750.0, 25570095.0, "GSM3909667 r1", "0:50", "A:334370606;C:306252389;G:299065406;T:338816349;N:0", 50, null, null, null, 334370606, 306252389, 299065406, 338816349, 0, "SRX6372828", "SRS5033893", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94373, null, 0.09279, null, 0.7191, null, 0.48836, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52950, "SRR9609433", "SRX6372827", "SRS5033892", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 3", "GSM3909666", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909666", "GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq", "GSM3909666", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909666", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1284828600.0, 25696572.0, "GSM3909666 r1", "0:50", "A:340467505;C:302914392;G:291984238;T:349462465;N:0", 50, null, null, null, 340467505, 302914392, 291984238, 349462465, 0, "SRX6372827", "SRS5033892", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94288, null, 0.0963, null, 0.71713, null, 0.4793, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52951, "SRR9609432", "SRX6372826", "SRS5033891", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 2", "GSM3909665", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909665", "GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq", "GSM3909665", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909665", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1274433150.0, 25488663.0, "GSM3909665 r1", "0:50", "A:336050330;C:303141446;G:297353928;T:337887446;N:0", 50, null, null, null, 336050330, 303141446, 297353928, 337887446, 0, "SRX6372826", "SRS5033891", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94266, null, 0.0966, null, 0.72476, null, 0.47615, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52952, "SRR9609431", "SRX6372825", "SRS5033890", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 1", "GSM3909664", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909664", "GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq", "GSM3909664", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909664", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1278273350.0, 25565467.0, "GSM3909664 r1", "0:50", "A:336762127;C:304299745;G:297929933;T:339281545;N:0", 50, null, null, null, 336762127, 304299745, 297929933, 339281545, 0, "SRX6372825", "SRS5033890", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94207, null, 0.09472, null, 0.72642, null, 0.47988, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [55655, "SRR10674410", "SRX7351703", "SRS5811186", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 100 1", null, "isolate:biologocal replicate 10|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050110", "bps050110", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_100_1_1.fq.gz BPS_100_1_2.fq.gz", "fastq fastq", 6958801200.0, 69588012.0, "BPS 100 1 1.fq.gz", "0:100 1:100", "A:1852139865;C:1635606671;G:1596180575;T:1874072794;N:801295", 100, 100, null, null, 1852139865, 1635606671, 1596180575, 1874072794, 801295, "SRX7351703", "SRS5811186", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94716, null, 0.09824, null, 0.68475, null, 0.47195, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55656, "SRR10674411", "SRX7351702", "SRS5811185", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 10 3", null, "isolate:biologocal replicate 9|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050109", "bps050109", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_10_3_1.fq.gz BPS_10_3_2.fq.gz", "fastq fastq", 6969574800.0, 69695748.0, "BPS 10 3 1.fq.gz", "0:100 1:100", "A:1860393053;C:1631995190;G:1597357772;T:1879188120;N:640665", 100, 100, null, null, 1860393053, 1631995190, 1597357772, 1879188120, 640665, "SRX7351702", "SRS5811185", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94597, null, 0.10542, null, 0.68016, null, 0.4666, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55657, "SRR10674412", "SRX7351701", "SRS5811182", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 10 2", null, "isolate:biologocal replicate 8|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050108", "bps050108", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_10_2_1.fq.gz BPS_10_2_2.fq.gz", "fastq fastq", 6709340400.0, 67093404.0, "BPS 10 2 1.fq.gz", "0:100 1:100", "A:2036224090;C:1319652145;G:1297564214;T:2055258677;N:641274", 100, 100, null, null, 2036224090, 1319652145, 1297564214, 2055258677, 641274, "SRX7351701", "SRS5811182", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.87778, null, 0.38111, null, 0.71543, null, 0.56061, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55658, "SRR10674413", "SRX7351700", "SRS5811181", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 10 1", null, "isolate:biologocal replicate 7|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050107", "bps050107", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_10_1_1.fq.gz BPS_10_1_2.fq.gz", "fastq fastq", 6717746800.0, 67177468.0, "BPS 10 1 1.fq.gz", "0:100 1:100", "A:1787637885;C:1578942212;G:1548400030;T:1802147201;N:619472", 100, 100, null, null, 1787637885, 1578942212, 1548400030, 1802147201, 619472, "SRX7351700", "SRS5811181", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94726, null, 0.10123, null, 0.68919, null, 0.45234, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55659, "SRR10674414", "SRX7351699", "SRS5811184", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1 3", null, "isolate:biologocal replicate 6|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050106", "bps050106", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1_3_2.fq.gz BPS_1_3_1.fq.gz", "fastq fastq", 6726522800.0, 67265228.0, "BPS 1 3 1.fq.gz", "0:100 1:100", "A:1789486049;C:1582069064;G:1548432478;T:1805913744;N:621465", 100, 100, null, null, 1789486049, 1582069064, 1548432478, 1805913744, 621465, "SRX7351699", "SRS5811184", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.9465, null, 0.09858, null, 0.68442, null, 0.45032, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55660, "SRR10674415", "SRX7351698", "SRS5811180", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1 2", null, "isolate:biologocal replicate 5|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050105", "bps050105", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1_2_2.fq.gz BPS_1_2_1.fq.gz", "fastq fastq", 6959685000.0, 69596850.0, "BPS 1 2 1.fq.gz", "0:100 1:100", "A:1914426129;C:1574998719;G:1542052351;T:1927550147;N:657654", 100, 100, null, null, 1914426129, 1574998719, 1542052351, 1927550147, 657654, "SRX7351698", "SRS5811180", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94034, null, 0.14574, null, 0.69934, null, 0.47033, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55661, "SRR10674416", "SRX7351697", "SRS5811183", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1 1", null, "isolate:biologocal replicate 4|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050104", "bps050104", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1_1_1.fq.gz BPS_1_1_2.fq.gz", "fastq fastq", 7040826400.0, 70408264.0, "BPS 1 1 1.fq.gz", "0:100 1:100", "A:1915125100;C:1612334047;G:1578924466;T:1933922418;N:520369", 100, 100, null, null, 1915125100, 1612334047, 1578924466, 1933922418, 520369, "SRX7351697", "SRS5811183", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94114, null, 0.13158, null, 0.68903, null, 0.47739, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55662, "SRR10674417", "SRX7351696", "SRS5811179", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 0 1 3", null, "isolate:biologocal replicate 3|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050103", "bps050103", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_0_1_3_1.fq.gz BPS_0_1_3_2.fq.gz", "fastq fastq", 6992676800.0, 69926768.0, "BPS 0 1 3 1.fq.gz", "0:100 1:100", "A:1860627581;C:1643489002;G:1610508221;T:1877536968;N:515028", 100, 100, null, null, 1860627581, 1643489002, 1610508221, 1877536968, 515028, "SRX7351696", "SRS5811179", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94485, null, 0.101, null, 0.68314, null, 0.45711, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55663, "SRR10674418", "SRX7351695", "SRS5811178", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "Cntrol3", null, "isolate:biologocal replicate 18|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050118", "bps050118", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol3_1.fq.gz Cntrol3_2.fq.gz", "fastq fastq", 6742983200.0, 67429832.0, "Cntrol3 1.fq.gz", "0:100 1:100", "A:1801392073;C:1577630219;G:1545614005;T:1817857809;N:489094", 100, 100, null, null, 1801392073, 1577630219, 1545614005, 1817857809, 489094, "SRX7351695", "SRS5811178", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94386, null, 0.10779, null, 0.68832, null, 0.45545, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55664, "SRR10674419", "SRX7351694", "SRS5811177", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "Cntrol2", null, "isolate:biologocal replicate 17|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050117", "bps050117", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol2_1.fq.gz Cntrol2_2.fq.gz", "fastq fastq", 6750661000.0, 67506610.0, "Cntrol2 1.fq.gz", "0:100 1:100", "A:1796606666;C:1585909518;G:1556014239;T:1811284557;N:846020", 100, 100, null, null, 1796606666, 1585909518, 1556014239, 1811284557, 846020, "SRX7351694", "SRS5811177", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94397, null, 0.10007, null, 0.68708, null, 0.47779, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55665, "SRR10674420", "SRX7351693", "SRS5811174", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "Cntrol1", null, "isolate:biologocal replicate 16|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050116", "bps050116", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol1_1.fq.gz Cntrol1_2.fq.gz", "fastq fastq", 6766663000.0, 67666630.0, "Cntrol1 1.fq.gz", "0:100 1:100", "A:1825736389;C:1564390057;G:1532835305;T:1842876742;N:824507", 100, 100, null, null, 1825736389, 1564390057, 1532835305, 1842876742, 824507, "SRX7351693", "SRS5811174", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94047, null, 0.12338, null, 0.68893, null, 0.46407, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55666, "SRR10674421", "SRX7351692", "SRS5811176", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1000 3", null, "isolate:biologocal replicate 15|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050115", "bps050115", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1000_3_1.fq.gz BPS_1000_3_2.fq.gz", "fastq fastq", 6507622200.0, 65076222.0, "BPS 1000 3 1.fq.gz", "0:100 1:100", "A:1735402948;C:1525938362;G:1493787016;T:1751945676;N:548198", 100, 100, null, null, 1735402948, 1525938362, 1493787016, 1751945676, 548198, "SRX7351692", "SRS5811176", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94304, null, 0.10593, null, 0.6842, null, 0.46348, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55667, "SRR10674422", "SRX7351691", "SRS5811173", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1000 2", null, "isolate:biologocal replicate 14|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050114", "bps050114", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1000_2_1.fq.gz BPS_1000_2_2.fq.gz", "fastq fastq", 6740712000.0, 67407120.0, "BPS 1000 2 1.fq.gz", "0:100 1:100", "A:1816870993;C:1562402111;G:1527381283;T:1833284067;N:773546", 100, 100, null, null, 1816870993, 1562402111, 1527381283, 1833284067, 773546, "SRX7351691", "SRS5811173", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94327, null, 0.11511, null, 0.70033, null, 0.4551, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55668, "SRR10674423", "SRX7351690", "SRS5811175", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 1000 1", null, "isolate:biologocal replicate 13|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050113", "bps050113", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1000_1_1.fq.gz BPS_1000_1_2.fq.gz", "fastq fastq", 6727750400.0, 67277504.0, "BPS 1000 1 1.fq.gz", "0:100 1:100", "A:1803578734;C:1568712705;G:1535618959;T:1819016739;N:823263", 100, 100, null, null, 1803578734, 1568712705, 1535618959, 1819016739, 823263, "SRX7351690", "SRS5811175", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94457, null, 0.1118, null, 0.69087, null, 0.46815, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55669, "SRR10674424", "SRX7351689", "SRS5811172", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 100 3", null, "isolate:biologocal replicate 12|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050112", "bps050112", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_100_3_1.fq.gz BPS_100_3_2.fq.gz", "fastq fastq", 6962431800.0, 69624318.0, "BPS 100 3 1.fq.gz", "0:100 1:100", "A:1865300693;C:1624120289;G:1585691091;T:1886538935;N:780792", 100, 100, null, null, 1865300693, 1624120289, 1585691091, 1886538935, 780792, "SRX7351689", "SRS5811172", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94581, null, 0.10195, null, 0.68288, null, 0.47174, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55670, "SRR10674425", "SRX7351688", "SRS5811171", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 100 2", null, "isolate:biologocal replicate 11|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050111", "bps050111", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_100_2_1.fq.gz BPS_100_2_2.fq.gz", "fastq fastq", 7201035800.0, 72010358.0, "BPS 100 2 1.fq.gz", "0:100 1:100", "A:2115590854;C:1489181336;G:1459936470;T:2135514629;N:812511", 100, 100, null, null, 2115590854, 1489181336, 1459936470, 2135514629, 812511, "SRX7351688", "SRS5811171", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.90678, null, 0.29289, null, 0.70735, null, 0.49554, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55671, "SRR10674426", "SRX7351687", "SRS5811170", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 0 1 2", null, "isolate:biologocal replicate 2|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050102", "bps050102", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_0_1_2_1.fq.gz BPS_0_1_2_2.fq.gz", "fastq fastq", 7022382800.0, 70223828.0, "BPS 0 1 2 1.fq.gz", "0:100 1:100", "A:1853514579;C:1663935080;G:1635277415;T:1869136960;N:518766", 100, 100, null, null, 1853514579, 1663935080, 1635277415, 1869136960, 518766, "SRX7351687", "SRS5811170", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94712, null, 0.09313, null, 0.6814, null, 0.47256, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55672, "SRR10674427", "SRX7351686", "SRS5811167", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "BPS 0 1 1", null, "isolate:biologocal replicate 1|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050101", "bps050101", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_0_1_1_1.fq.gz BPS_0_1_1_2.fq.gz", "fastq fastq", 7013900400.0, 70139004.0, "BPS 0 1 1 1.fq.gz", "0:100 1:100", "A:1885826391;C:1629114228;G:1597181244;T:1901261511;N:517026", 100, 100, null, null, 1885826391, 1629114228, 1597181244, 1901261511, 517026, "SRX7351686", "SRS5811167", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94226, null, 0.11616, null, 0.69014, null, 0.45679, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [57168, "SRR11237928", "SRX7849591", "SRS6259054", "SRP251591", "PRJNA610302", "Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development", "GSE146394", "Transcriptome Analysis", "To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology", null, null, null, "MZ 7hpf Dome", "GSM4379949", null, "source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ", "MZ 7hpf Dome", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", null, "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ", "GSM4379949", "GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq", "GSM4379949", null, "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", "GEO Accession:GSM4379949", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP251591", null, null, "MZ_7h_Dome_1.fq.gz", "fastq", 1065702100.0, 21314042.0, "GSM4379949 r1", "0:50 1:0", "A:283324952;C:247492025;G:242059243;T:291819466;N:1006414", 50, 0, null, null, 283324952, 247492025, 242059243, 291819466, 1006414, "SRX7849591", "SRS6259054", "SRA1051151", "GEO", "School of life science, Tsinghua University", 1, 0.9445, null, 0.07752, null, 0.72565, null, 0.4828, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [57169, "SRR11237927", "SRX7849590", "SRS6259053", "SRP251591", "PRJNA610302", "Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development", "GSE146394", "Transcriptome Analysis", "To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology", null, null, null, "MZ 4.3hpf 1k", "GSM4379948", null, "source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ", "MZ 4.3hpf 1k", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", null, "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ", "GSM4379948", "GSM4379948: MZ 4.3hpf 1k; Danio rerio; RNA Seq", "GSM4379948", null, "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", "GEO Accession:GSM4379948", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP251591", null, null, "MZ_4.3h_1k_1.fq.gz", "fastq", 1059959500.0, 21199190.0, "GSM4379948 r1", "0:50 1:0", "A:278456455;C:249622199;G:244991579;T:285847713;N:1041554", 50, 0, null, null, 278456455, 249622199, 244991579, 285847713, 1041554, "SRX7849590", "SRS6259053", "SRA1051151", "GEO", "School of life science, Tsinghua University", 1, 0.94882, null, 0.03659, null, 0.74361, null, 0.48435, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [57170, "SRR11237926", "SRX7849589", "SRS6259052", "SRP251591", "PRJNA610302", "Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development", "GSE146394", "Transcriptome Analysis", "To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology", null, null, null, "WT 4.3hpf Dome", "GSM4379947", null, "source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type", "WT 4.3hpf Dome", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", null, "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type", "GSM4379947", "GSM4379947: WT 4.3hpf Dome; Danio rerio; RNA Seq", "GSM4379947", null, "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", "GEO Accession:GSM4379947", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP251591", null, null, "WT_4.3h_Dome_1.fq.gz", "fastq", 1058158950.0, 21163179.0, "GSM4379947 r1", "0:50 1:0", "A:279307143;C:247873321;G:244308380;T:285580565;N:1089541", 50, 0, null, null, 279307143, 247873321, 244308380, 285580565, 1089541, "SRX7849589", "SRS6259052", "SRA1051151", "GEO", "School of life science, Tsinghua University", 1, 0.94374, null, 0.05294, null, 0.74164, null, 0.48705, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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"], [60445, "SRR12272862", "SRX8777892", "SRS7048444", "SRP272672", "PRJNA647444", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA", "PRJNA647444", "Other", "Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.", null, null, null, "C2", "C2 C2 2 4", null, "replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2C220200712", "C2C220200712", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "loader:fastq 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the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.", null, null, null, "C2", "C2 C2 1 4", null, "replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2C220200711", "C2C220200711", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "loader:fastq load.py", "C2_C2_1_4.fq", "fastq", 542847476.0, 22614181.0, "C2 C2 1 4.fq.gz", "0:24.00", "A:99999101;C:125407906;G:162383758;T:155055099;N:1612", 24, null, null, null, 99999101, 125407906, 162383758, 155055099, 1612, "SRX8777891", "SRS7048443", "SRA1101037", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.84327, null, 0.10491, null, 0.83256, null, 0.52046, null, 19, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-08-05", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [60447, "SRR12272864", "SRX8777890", "SRS7048442", "SRP272672", "PRJNA647444", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA", "PRJNA647444", "Other", "Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic 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"Undetermined", "Embryo", "Whole Organism", "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"], [60613, "SRR12435888", "SRX8931583", "SRS7187991", "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 24hpf  replicate 2", "GSM4724530", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 24hpf  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:24 hpf|genotype:WT", "GSM4724530", "GSM4724530: RNA seq in zebrafish wild type embryos at 24hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724530", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724530", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_wt_rep2_1.fq.gz", "fastq", 2241073250.0, 44821465.0, "GSM4724530 r1", "0:50", "A:593435654;C:517470954;G:544866646;T:585299996;N:0", 50, null, null, null, 593435654, 517470954, 544866646, 585299996, 0, "SRX8931583", "SRS7187991", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.9534, null, 0.07821, null, 0.70331, null, 0.47463, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [60614, "SRR12435887", "SRX8931582", "SRS7187990", "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 24hpf  replicate 1", "GSM4724529", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 24hpf  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:24 hpf|genotype:WT", "GSM4724529", "GSM4724529: RNA seq in zebrafish wild type embryos at 24hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724529", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_wt_rep1_1.fq.gz", "fastq", 1206103900.0, 24122078.0, "GSM4724529 r1", "0:50", "A:329983157;C:268788282;G:289794374;T:316858580;N:679507", 50, null, null, null, 329983157, 268788282, 289794374, 316858580, 679507, "SRX8931582", "SRS7187990", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94221, null, 0.09615, null, 0.69077, null, 0.47405, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [60615, "SRR12435886", "SRX8931581", "SRS7187989", "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 24hpf  replicate 2", "GSM4724528", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 24hpf  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:24 hpf|genotype:ctcf  / ", "GSM4724528", "GSM4724528: RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724528", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_ctcf_rep2_1.fq.gz", "fastq", 2823674750.0, 56473495.0, "GSM4724528 r1", "0:50", "A:743759446;C:653943934;G:679405104;T:746566266;N:0", 50, null, null, null, 743759446, 653943934, 679405104, 746566266, 0, "SRX8931581", "SRS7187989", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95027, null, 0.08763, null, 0.6984, null, 0.487, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [60616, "SRR12435885", "SRX8931580", "SRS7187988", "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 24hpf  replicate 1", "GSM4724527", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 24hpf  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:24 hpf|genotype:ctcf  / ", "GSM4724527", "GSM4724527: RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724527", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_ctcf_rep1_1.fq.gz", "fastq", 2408631250.0, 48172625.0, "GSM4724527 r1", "0:50", "A:623761639;C:570722378;G:584932664;T:629214569;N:0", 50, null, null, null, 623761639, 570722378, 584932664, 629214569, 0, "SRX8931580", "SRS7187988", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95366, null, 0.07765, null, 0.70023, null, 0.47375, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [61503, "SRR12780056", "SRX9249644", "SRS7482118", "SRP286526", "PRJNA667677", "Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish", "GSE159087", "Transcriptome Analysis", "Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf  embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ  in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.", null, null, null, "phf tMO 4.7h", "GSM4819005", null, "tissue:embryos|strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "phf tMO 4.7h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al.  nature method  2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples", "embryos", "Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Embryos were cultured in the holfretor water.", "strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "GSM4819005", "GSM4819005: phf tMO 4.7h; Danio rerio; RNA Seq", "GSM4819005", null, "1", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4819005", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP286526", null, null, "phf_tMO_4.7h.fq.gz", "fastq", 1169147800.0, 23382956.0, "GSM4819005 r1", "0:50", "A:311605612;C:272452820;G:269040332;T:316049036;N:0", 50, null, null, null, 311605612, 272452820, 269040332, 316049036, 0, "SRX9249644", "SRS7482118", "SRA1139165", "GEO", "Haitao Li, School of medicine, Tsinghua University", 1, 0.94966, null, 0.07252, null, 0.73651, null, 0.49931, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [61504, "SRR12780055", "SRX9249643", "SRS7482117", "SRP286526", "PRJNA667677", "Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish", "GSE159087", "Transcriptome Analysis", "Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf  embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ  in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.", null, null, null, "std MO 4.7h", "GSM4819004", null, "tissue:embryos|strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "std MO 4.7h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al.  nature method  2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples", "embryos", "Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Embryos were cultured in the holfretor water.", "strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "GSM4819004", "GSM4819004: std MO 4.7h; Danio rerio; RNA Seq", "GSM4819004", null, "1", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4819004", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP286526", null, null, "std_MO_4.7h.fq.gz", "fastq", 1169210150.0, 23384203.0, "GSM4819004 r1", "0:50", "A:311848924;C:271805947;G:268541126;T:317014153;N:0", 50, null, null, null, 311848924, 271805947, 268541126, 317014153, 0, "SRX9249643", "SRS7482117", "SRA1139165", "GEO", "Haitao Li, School of medicine, Tsinghua University", 1, 0.94838, null, 0.07833, null, 0.74192, null, 0.48213, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [65852, "SRR15657174", "SRX11954177", "SRS9963999", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.156uM 96hpf", "GSM5543529", null, "tissue:embryo  Cu 0.156uM 96hpf|cell type:embryos at 96hpf whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.156uM 96hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.156uM 96hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 96hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543529", "GSM5543529: embryo Cu 0.156uM 96hpf; Danio rerio; RNA Seq", "GSM5543529", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.156uM_96hpf_R1.fastq.gz Cu_0.156uM_96hpf_R2.fastq.gz", "fastq fastq", 7167443000.0, 71674430.0, "GSM5543529 r1", "0:100 1:100", "A:1930084120;C:1646651059;G:1623549050;T:1966203424;N:955347", 100, 100, null, null, 1930084120, 1646651059, 1623549050, 1966203424, 955347, "SRX11954177", "SRS9963999", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94339, null, 0.113, null, 0.6549, null, 0.4857, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65853, "SRR15657173", "SRX11954176", "SRS9963998", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.156uM 24hpf", "GSM5543528", null, "tissue:embryo  Cu 0.156uM 24hpf|cell type:embryos at 24hpf whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.156uM 24hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.156uM 24hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 24hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.156\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543528", "GSM5543528: embryo Cu 0.156uM 24hpf; Danio rerio; RNA Seq", "GSM5543528", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.156uM_24hpf_R1.fastq.gz Cu_0.156uM_24hpf_R2.fastq.gz", "fastq fastq", 7164832400.0, 71648324.0, "GSM5543528 r1", "0:100 1:100", "A:1929135591;C:1646939515;G:1617401036;T:1970900148;N:456110", 100, 100, null, null, 1929135591, 1646939515, 1617401036, 1970900148, 456110, "SRX11954176", "SRS9963998", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94344, null, 0.10713, null, 0.68919, null, 0.47118, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65854, "SRR15657172", "SRX11954175", "SRS9963997", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.078uM 96hpf", "GSM5543527", null, "tissue:embryo  Cu 0.078uM 96hpf|cell type:embryos at 96hpf whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.078uM 96hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.078uM 96hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 96hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543527", "GSM5543527: embryo Cu 0.078uM 96hpf; Danio rerio; RNA Seq", "GSM5543527", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.078uM_96hpf_R1.fastq.gz Cu_0.078uM_96hpf_R2.fastq.gz", "fastq fastq", 7135774800.0, 71357748.0, "GSM5543527 r1", "0:100 1:100", "A:1928230196;C:1633490990;G:1605871113;T:1967776814;N:405687", 100, 100, null, null, 1928230196, 1633490990, 1605871113, 1967776814, 405687, "SRX11954175", "SRS9963997", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94191, null, 0.11803, null, 0.65614, null, 0.48225, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [65855, "SRR15657171", "SRX11954174", "SRS9963995", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Cu 0.078uM 24hpf", "GSM5543526", null, "tissue:embryo  Cu 0.078uM 24hpf|cell type:embryos at 24hpf whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Cu 0.078uM 24hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Cu 0.078uM 24hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 24hpf hours post  fertilization|treatment:embryos whose parents were exposed to 0.078\u03bcM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543526", "GSM5543526: embryo Cu 0.078uM 24hpf; Danio rerio; RNA Seq", "GSM5543526", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Cu_0.078uM_24hpf_R1.fastq.gz Cu_0.078uM_24hpf_R2.fastq.gz", "fastq fastq", 6934019600.0, 69340196.0, "GSM5543526 r1", "0:100 1:100", "A:1865548284;C:1597354050;G:1569395022;T:1901304271;N:417973", 100, 100, null, null, 1865548284, 1597354050, 1569395022, 1901304271, 417973, "SRX11954174", "SRS9963995", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.94389, null, 0.10356, null, 0.68726, null, 0.47794, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 209, "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", 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