{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", 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"], [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 . 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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. 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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. 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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. 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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"], [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"], [60496, "SRR12328853", "SRX8829078", "SRS7048444", "SRP273655", "PRJNA648800", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA", "PRJNA648800", "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, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP273655", null, null, "C2_C2_2_4_1.fq.gz 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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 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, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP273655", null, null, "C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz", "fastq fastq", 6942905200.0, 69429052.0, "C2 C2 1 4 1.fq.gz", "0:100 1:100", "A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0", 100, 100, null, null, 2025129308, 1433430820, 1434784226, 2049560846, 0, "SRX8829077", "SRS7048443", "SRA1103962", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93211, null, 0.16662, null, 0.71001, null, 0.53674, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-27", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [60498, "SRR12328855", "SRX8829076", "SRS7048442", "SRP273655", "PRJNA648800", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA", "PRJNA648800", "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, "C1", "C1 C1 2 4", null, "replicate:biological replicate 2|strain:AB|isolate:C1|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:1ug/L|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1C120200712", "C1C120200712", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP273655", null, null, "C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz", "fastq fastq", 6973657600.0, 69736576.0, "C1 C1 2 4 1.fq.gz", "0:100 1:100", "A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0", 100, 100, null, null, 2050440259, 1423350359, 1423015668, 2076851314, 0, "SRX8829076", "SRS7048442", "SRA1103962", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.92911, null, 0.1877, null, 0.72025, null, 0.58085, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-27", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [60499, "SRR12328856", "SRX8829075", "SRS7048441", "SRP273655", "PRJNA648800", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA", "PRJNA648800", "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, "C1", "C1 C1 1 4", null, "replicate:biological replicate 1|strain:AB|isolate:C1|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:1ug/L|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1C120200711", "C1C120200711", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP273655", null, null, "C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz", "fastq fastq", 6746729200.0, 67467292.0, "C1 C1 1 4 1.fq.gz", "0:100 1:100", "A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0", 100, 100, null, null, 2004203843, 1356765594, 1357760526, 2027999237, 0, "SRX8829075", "SRS7048441", "SRA1103962", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.92733, null, 0.19903, null, 0.72228, null, 0.59259, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-27", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [60500, "SRR12328857", "SRX8829074", "SRS7048440", "SRP273655", "PRJNA648800", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA", "PRJNA648800", "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, "C0", "C0 C0 2 4", null, "replicate:biological replicate 2|strain:AB|isolate:C0|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:0ug/L|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0C020200712", "C0C020200712", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP273655", null, null, "C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz", "fastq fastq", 6924724800.0, 69247248.0, "C0 C0 2 4 1.fq.gz", "0:100 1:100", "A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0", 100, 100, null, null, 1974618038, 1471821932, 1482725702, 1995559128, 0, "SRX8829074", "SRS7048440", "SRA1103962", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93473, null, 0.14676, null, 0.69649, null, 0.50413, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-27", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [60501, "SRR12328858", "SRX8829073", "SRS7048439", "SRP273655", "PRJNA648800", "mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA", "PRJNA648800", "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, "C0", "C0 C0 1 4", null, "replicate:biological replicate 1|strain:AB|isolate:C0|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:0ug/L|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0C020200711", "C0C020200711", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP273655", null, null, "C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz", "fastq fastq", 6899505600.0, 68995056.0, "C0 C0 1 4 1.fq.gz", "0:100 1:100", "A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0", 100, 100, null, null, 1957459931, 1477351919, 1482435319, 1982258431, 0, "SRX8829073", "SRS7048439", "SRA1103962", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93567, null, 0.14057, null, 0.6883, null, 0.48707, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-07-27", "Undetermined", "Embryo", "Whole Organism", "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"], [65856, "SRR15657170", "SRX11954173", "SRS9963996", "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 Control 96hpf", "GSM5543525", null, "tissue:embryo  Control 96hpf|cell type:embryos at 96hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Control 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  Control 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 normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543525", "GSM5543525: embryo Control 96hpf; Danio rerio; RNA Seq", "GSM5543525", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Control_96hpf_R1.fastq.gz Control_96hpf_R2.fastq.gz", "fastq fastq", 6698614400.0, 66986144.0, "GSM5543525 r1", "0:100 1:100", "A:1816763075;C:1526218454;G:1496202651;T:1858550518;N:879702", 100, 100, null, null, 1816763075, 1526218454, 1496202651, 1858550518, 879702, "SRX11954173", "SRS9963996", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.93836, null, 0.12432, null, 0.65504, null, 0.47564, 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"], [65857, "SRR15657169", "SRX11954172", "SRS9963994", "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 Control 24hpf", "GSM5543524", null, "tissue:embryo  Control 24hpf|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Control 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  Control 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 normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543524", "GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq", "GSM5543524", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz", "fastq fastq", 6911559200.0, 69115592.0, "GSM5543524 r1", "0:100 1:100", "A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486", 100, 100, null, null, 1858569189, 1592355971, 1564572369, 1895593185, 468486, "SRX11954172", "SRS9963994", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.93745, null, 0.09795, null, 0.69059, null, 0.48209, 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"], [65984, "SRR15859821", "SRX12150937", "SRS10130028", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "levonorgestrel treatment at high concentration treatment", "LNG H 1", "AN", null, "strain:not collected2|isolate:whole fish13|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 1'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LNG H 1", "BM", "BM", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "50_1_R1.clean.fq.gz 50_1_R2.clean.fq.gz", "fastq fastq", 6850889266.0, 22893917.0, "50 1 R1.clean.fq.gz", "0:149.83 1:149.42", "A:1908972876;C:1556853849;G:1559240564;T:1825804841;N:17136", 149, 149, null, null, 1908972876, 1556853849, 1559240564, 1825804841, 17136, "SRX12150937", "SRS10130028", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.93957, 0.92386, 0.09467, 0.08944, 0.66582, 0.67142, 0.50349, 0.499, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [65985, "SRR15859822", "SRX12150936", "SRS10130027", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "levonorgestrel treatment at low concentration treatment", "LNG L 4", "M", null, "strain:not collected2|isolate:whole fish12|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 4'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LNG L 4", "BL", "BL", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "5_4_R1.clean.fq.gz 5_4_R2.clean.fq.gz", "fastq fastq", 6757301758.0, 22579367.0, "5 4 R1.clean.fq.gz", "0:149.83 1:149.44", "A:1886236851;C:1526321374;G:1529138861;T:1815587663;N:17009", 149, 149, null, null, 1886236851, 1526321374, 1529138861, 1815587663, 17009, "SRX12150936", "SRS10130027", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.93955, 0.92322, 0.09955, 0.0937, 0.66612, 0.67056, 0.4936, 0.50296, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [65986, "SRR15859823", "SRX12150935", "SRS10130026", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "levonorgestrel treatment at low concentration treatment", "LNG L 3", "AL", null, "strain:not collected2|isolate:whole fish11|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 3 prime|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LNG L 3", "BK", "BK", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "5_3_R1.clean.fq.gz 5_3_R2.clean.fq.gz", "fastq fastq", 6942028867.0, 23178890.0, "5 3 R1.clean.fq.gz", "0:149.82 1:149.68", "A:1895507796;C:1573477638;G:1599422601;T:1873160988;N:459844", 149, 149, null, null, 1895507796, 1573477638, 1599422601, 1873160988, 459844, "SRX12150935", "SRS10130026", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.92261, 0.9213, 0.10308, 0.10394, 0.67298, 0.67677, 0.50615, 0.5026, 150, 145, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [65987, "SRR15859824", "SRX12150934", "SRS10130025", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "Solvent control", "SC2", "AC", null, "strain:not collected2|isolate:whole fish2|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 2'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "SC2", "BB", "BB", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "SC_2_R1.clean.fq.gz SC_2_R2.clean.fq.gz", "fastq fastq", 6847074418.0, 22905359.0, "SC 2 R1.clean.fq.gz", "0:149.58 1:149.35", "A:1835075664;C:1586631096;G:1607651961;T:1817247855;N:467842", 149, 149, null, null, 1835075664, 1586631096, 1607651961, 1817247855, 467842, "SRX12150934", "SRS10130025", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.93172, 0.93195, 0.07691, 0.0771, 0.67265, 0.67665, 0.48862, 0.49579, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [65988, "SRR15859825", "SRX12150933", "SRS10130024", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "Solvent control", "SC1", "AB", null, "strain:not collected2|isolate:whole fish1|breed:not collected|cultivar:not 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collected2|isolate:whole fish19|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 3 prime|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DDG+LNG L 3", "BS", "BS", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "100_5_3_R1.clean.fq.gz 100_5_3_R2.clean.fq.gz", "fastq fastq", 6731263096.0, 22494392.0, "100 5 3 R1.clean.fq.gz", "0:149.82 1:149.42", "A:1853865687;C:1546635036;G:1549005691;T:1781740007;N:16675", 149, 149, null, null, 1853865687, 1546635036, 1549005691, 1781740007, 16675, "SRX12150919", "SRS10130010", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.94161, 0.92699, 0.09368, 0.08881, 0.67146, 0.67671, 0.49075, 0.4916, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [66003, "SRR15859840", "SRX12150918", "SRS10130009", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "Levonorgestrel  at low concentration and dydrogesterone mixtures treatment", "DDG+LNG L 2", "AS", null, "strain:not collected2|isolate:whole fish18|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 2'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DDG+LNG L 2", "BR", "BR", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "100_5_2_R1.clean.fq.gz 100_5_2_R2.clean.fq.gz", "fastq fastq", 6856677730.0, 22942302.0, "100 5 2 R1.clean.fq.gz", "0:149.63 1:149.23", "A:1861833177;C:1593702006;G:1601437245;T:1799688067;N:17235", 149, 149, null, null, 1861833177, 1593702006, 1601437245, 1799688067, 17235, "SRX12150918", "SRS10130009", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.94226, 0.93085, 0.08471, 0.08039, 0.67677, 0.68191, 0.48927, 0.47969, 150, 148, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [66004, "SRR15859841", "SRX12150917", "SRS10130007", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "Levonorgestrel  at low concentration and dydrogesterone mixtures treatment", "DDG+LNG L 1", "AR", null, "strain:not collected2|isolate:whole fish17|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 1'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DDG+LNG L 1", "BQ", "BQ", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "100_5_1_R1.clean.fq.gz 100_5_1_R2.clean.fq.gz", "fastq fastq", 6734596961.0, 22519168.0, "100 5 1 R1.clean.fq.gz", "0:149.72 1:149.34", "A:1835515639;C:1562058332;G:1561380426;T:1775625709;N:16855", 149, 149, null, null, 1835515639, 1562058332, 1561380426, 1775625709, 16855, "SRX12150917", "SRS10130007", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.94108, 0.92768, 0.09123, 0.08716, 0.66967, 0.6747, 0.50584, 0.50347, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [66005, "SRR15859842", "SRX12150916", "SRS10130006", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "levonorgestrel treatment at high concentration treatment", "LNG H 4", "AQ", null, "strain:not collected2|isolate:whole fish16|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 4'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LNG H 4", "BP", "BP", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "50_4_R1.clean.fq.gz 50_4_R2.clean.fq.gz", "fastq fastq", 7033955938.0, 23502039.0, "50 4 R1.clean.fq.gz", "0:149.84 1:149.46", "A:1939982949;C:1612770444;G:1610988374;T:1870196531;N:17640", 149, 149, null, null, 1939982949, 1612770444, 1610988374, 1870196531, 17640, "SRX12150916", "SRS10130006", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.94099, 0.92749, 0.09644, 0.09215, 0.67261, 0.67838, 0.49766, 0.49584, 150, 149, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [66006, "SRR15859843", "SRX12150915", "SRS10130008", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "levonorgestrel treatment at high concentration treatment", "LNG H 3", "AP", null, "strain:not collected2|isolate:whole fish15|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 3 prime|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LNG H 3", "BO", "BO", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "50_3_R1.clean.fq.gz 50_3_R2.clean.fq.gz", "fastq fastq", 5819952570.0, 19444342.0, "50 3 R1.clean.fq.gz", "0:149.86 1:149.46", "A:1615559082;C:1328350353;G:1325535770;T:1550492661;N:14704", 149, 149, null, null, 1615559082, 1328350353, 1325535770, 1550492661, 14704, "SRX12150915", "SRS10130008", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.9397, 0.92495, 0.09375, 0.08838, 0.669, 0.67338, 0.50535, 0.5146, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [66007, "SRR15859844", "SRX12150914", "SRS10130005", "SRP336743", "PRJNA760976", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA760976", "Transcriptome Analysis", "we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish", null, null, "levonorgestrel treatment at high concentration treatment", "LNG H 2", "AO", null, "strain:not collected2|isolate:whole fish14|breed:not collected|cultivar:not applicable3|ecotype:not applicable4|age:4 weeks|dev stage:not applicable5|sex:missing|tissue:whole fish|replicate:'replicate = biological replicate 2'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LNG H 2", "BN", "BN", "zebraifsh exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP336743", null, null, "50_2_R1.clean.fq.gz 50_2_R2.clean.fq.gz", "fastq fastq", 5888497480.0, 19673249.0, "50 2 R1.clean.fq.gz", "0:149.84 1:149.47", "A:1638307115;C:1337036459;G:1335389572;T:1577749137;N:15197", 149, 149, null, null, 1638307115, 1337036459, 1335389572, 1577749137, 15197, "SRX12150914", "SRS10130005", "SRA1291484", "South China Normal University|School of Environment", "South China Normal University", 2, 0.9395, 0.92471, 0.09382, 0.08964, 0.66785, 0.67144, 0.50388, 0.5077, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-09-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67043, "SRR17017805", "SRX13207904", "SRS11133999", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1  /  KO la3", "GSM5701222", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "Aldh 2.1  /  KO la3", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "GSM5701222", "GSM5701222: Aldh 2.1  /  KO la3; Danio rerio; RNA Seq", "GSM5701222 r1", "GSM5701222", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "3-KOla3_1.fq.gz 3-KOla3_2.fq.gz", "fastq fastq", 4974883400.0, 49748834.0, "GSM5701222 r1", "0:100 1:100", "A:1325503000;C:1131322113;G:1183075417;T:1334982870;N:0", 100, 100, null, null, 1325503000, 1131322113, 1183075417, 1334982870, 0, "SRX13207904", "SRS11133999", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.95156, null, 0.10103, null, 0.68917, null, 0.50967, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67044, "SRR17017806", "SRX13207903", "SRS11133998", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1  /  KO la2", "GSM5701221", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "Aldh 2.1  /  KO la2", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "GSM5701221", "GSM5701221: Aldh 2.1  /  KO la2; Danio rerio; RNA Seq", "GSM5701221 r1", "GSM5701221", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "2-KOla2_1.fq.gz 2-KOla2_2.fq.gz", "fastq fastq", 4993502200.0, 49935022.0, "GSM5701221 r1", "0:100 1:100", "A:1337290403;C:1130744731;G:1181303599;T:1344163467;N:0", 100, 100, null, null, 1337290403, 1130744731, 1181303599, 1344163467, 0, "SRX13207903", "SRS11133998", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.95056, null, 0.09273, null, 0.69207, null, 0.5213, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67045, "SRR17017807", "SRX13207902", "SRS11133997", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1  /  KO la1", "GSM5701220", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "Aldh 2.1  /  KO la1", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "GSM5701220", "GSM5701220: Aldh 2.1  /  KO la1; Danio rerio; RNA Seq", "GSM5701220 r1", "GSM5701220", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "1-KOla1_1.fq.gz 1-KOla1_2.fq.gz", "fastq fastq", 4982824800.0, 49828248.0, "GSM5701220 r1", "0:100 1:100", "A:1318751230;C:1142967126;G:1194575929;T:1326530515;N:0", 100, 100, null, null, 1318751230, 1142967126, 1194575929, 1326530515, 0, "SRX13207902", "SRS11133997", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.95468, null, 0.09398, null, 0.67917, null, 0.50026, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67046, "SRR17017808", "SRX13207901", "SRS11133996", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1 +/+ WT la6", "GSM5701229", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "Aldh 2.1 +/+ WT la6", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "GSM5701229", "GSM5701229: Aldh 2.1 +/+ WT la6; Danio rerio; RNA Seq", "GSM5701229 r1", "GSM5701229", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "10-WTla6_1.fq.gz 10-WTla6_2.fq.gz", "fastq fastq", 4990544400.0, 49905444.0, "GSM5701229 r1", "0:100 1:100", "A:1342332744;C:1123081871;G:1174336584;T:1350793201;N:0", 100, 100, null, null, 1342332744, 1123081871, 1174336584, 1350793201, 0, "SRX13207901", "SRS11133996", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.94932, null, 0.10692, null, 0.69246, null, 0.5131, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67047, "SRR17017809", "SRX13207900", "SRS11133995", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1 +/+ WT la5", "GSM5701228", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "Aldh 2.1 +/+ WT la5", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "GSM5701228", "GSM5701228: Aldh 2.1 +/+ WT la5; Danio rerio; RNA Seq", "GSM5701228 r1", "GSM5701228", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "9-WTla5_1.fq.gz 9-WTla5_2.fq.gz", "fastq fastq", 4990444600.0, 49904446.0, "GSM5701228 r1", "0:100 1:100", "A:1347054785;C:1118741393;G:1169087601;T:1355560821;N:0", 100, 100, null, null, 1347054785, 1118741393, 1169087601, 1355560821, 0, "SRX13207900", "SRS11133995", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.94929, null, 0.10427, null, 0.69925, null, 0.51838, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67048, "SRR17017810", "SRX13207899", "SRS11133994", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1 +/+ WT la3", "GSM5701227", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "Aldh 2.1 +/+ WT la3", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "GSM5701227", "GSM5701227: Aldh 2.1 +/+ WT la3; Danio rerio; RNA Seq", "GSM5701227 r1", "GSM5701227", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "8-WTla3_1.fq.gz 8-WTla3_2.fq.gz", "fastq fastq", 4986064600.0, 49860646.0, "GSM5701227 r1", "0:100 1:100", "A:1358143440;C:1107981393;G:1154357851;T:1365581916;N:0", 100, 100, null, null, 1358143440, 1107981393, 1154357851, 1365581916, 0, "SRX13207899", "SRS11133994", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.95037, null, 0.10323, null, 0.69499, null, 0.54725, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67049, "SRR17017811", "SRX13207898", "SRS11133993", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1 +/+ WT la2", "GSM5701226", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "Aldh 2.1 +/+ WT la2", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "GSM5701226", "GSM5701226: Aldh 2.1 +/+ WT la2; Danio rerio; RNA Seq", "GSM5701226 r1", "GSM5701226", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "7-WTla2_1.fq.gz 7-WTla2_2.fq.gz", "fastq fastq", 4977068600.0, 49770686.0, "GSM5701226 r1", "0:100 1:100", "A:1341174868;C:1117869236;G:1167898570;T:1350125926;N:0", 100, 100, null, null, 1341174868, 1117869236, 1167898570, 1350125926, 0, "SRX13207898", "SRS11133993", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.94822, null, 0.11063, null, 0.69514, null, 0.51197, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67050, "SRR17017812", "SRX13207897", "SRS11133992", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1 +/+ WT la1", "GSM5701225", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "Aldh 2.1 +/+ WT la1", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:WT", "GSM5701225", "GSM5701225: Aldh 2.1 +/+ WT la1; Danio rerio; RNA Seq", "GSM5701225 r1", "GSM5701225", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "6-WTla1_1.fq.gz 6-WTla1_2.fq.gz", "fastq fastq", 4937740400.0, 49377404.0, "GSM5701225 r1", "0:100 1:100", "A:1322363529;C:1116877989;G:1169055598;T:1329443284;N:0", 100, 100, null, null, 1322363529, 1116877989, 1169055598, 1329443284, 0, "SRX13207897", "SRS11133992", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.95215, null, 0.10081, null, 0.69534, null, 0.51784, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67051, "SRR17017813", "SRX13207896", "SRS11133991", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1  /  KO la6", "GSM5701224", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "Aldh 2.1  /  KO la6", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "GSM5701224", "GSM5701224: Aldh 2.1  /  KO la6; Danio rerio; RNA Seq", "GSM5701224 r1", "GSM5701224", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "5-KOla6_1.fq.gz 5-KOla6_2.fq.gz", "fastq fastq", 4875673200.0, 48756732.0, "GSM5701224 r1", "0:100 1:100", "A:1325527276;C:1084173307;G:1132675639;T:1333296978;N:0", 100, 100, null, null, 1325527276, 1084173307, 1132675639, 1333296978, 0, "SRX13207896", "SRS11133991", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.94517, null, 0.10711, null, 0.69548, null, 0.47813, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67052, "SRR17017814", "SRX13207895", "SRS11133990", "SRP347444", "PRJNA782975", "Accumulation of Acetaldehyde in aldh2.1 /  Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis", "GSE189416", "Transcriptome Analysis", "In conclusion  the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover  Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 /  zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification  metabolomics  genomics and organ health   especially vascular health.", null, "pubmed:35114580", null, "Aldh 2.1  /  KO la5", "GSM5701223", null, "source name:whole larvae|developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "Aldh 2.1  /  KO la5", "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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "whole larvae", null, "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Embryos / larvae were held and raised in egg water at 28.5 \u00b0C for 120 hours with no extra treatment.", "developmental stage:larvae 120hpf|tissue:whole larvae|genotype:aldh2.1 knockout", "GSM5701223", "GSM5701223: Aldh 2.1  /  KO la5; Danio rerio; RNA Seq", "GSM5701223 r1", "GSM5701223", "1", "Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf  collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP347444", null, null, "4-KOla5_1.fq.gz 4-KOla5_2.fq.gz", "fastq fastq", 4965270200.0, 49652702.0, "GSM5701223 r1", "0:100 1:100", "A:1348940910;C:1104562620;G:1155269060;T:1356497610;N:0", 100, 100, null, null, 1348940910, 1104562620, 1155269060, 1356497610, 0, "SRX13207895", "SRS11133990", "SRA1492011", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 1, 0.94849, null, 0.11019, null, 0.69988, null, 0.53589, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-11-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67884, "SRR17868935", "SRX14028691", "SRS11864778", "SRP358022", "PRJNA793391", "Effects of acute exposure to nano silver on zebrafish larvae", "PRJNA793391", "Other", "Sliver nanoparticles AgNPs are widely used for industry  agriculture  and medicals  which potentially result in adverse effects for human health and aquatic environment. In this present study  we investigated  the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.", null, null, null, null, "C4 1", null, "strain:danio rerio AgNPs4|breed:zebrafish10|age:3 day|sex:pooled male and female|tissue:fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DANIO RERIO 4 1", "AG 4 1", "AG 4 1", "treatment7", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C4-1_1.fq.gz C4-1_2.fq.gz", "fastq fastq", 6830916900.0, 45539446.0, "C4 1 1.fq.gz", "0:150 1:150", "A:2011586443;C:1405775454;G:1388504965;T:2024992696;N:57342", 150, 150, null, null, 2011586443, 1405775454, 1388504965, 2024992696, 57342, "SRX14028691", "SRS11864778", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.92344, null, 0.21929, null, 0.71043, null, 0.46315, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67885, "SRR17868936", "SRX14028690", "SRS11864777", "SRP358022", "PRJNA793391", "Effects of acute exposure to nano silver on zebrafish larvae", "PRJNA793391", "Other", "Sliver nanoparticles AgNPs are widely used for industry  agriculture  and medicals  which potentially result in adverse effects for human health and aquatic environment. 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In this present study  we investigated  the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.", null, null, null, null, "C2 2", null, "strain:danio rerio AgNPs2|breed:zebrafish8|age:3 day|sex:pooled male and female|tissue:fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DANIO RERIO 2 2", "AG 2 2", "AG 2 2", "treatment5", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C2-2_1.fq.gz C2-2_2.fq.gz", "fastq fastq", 6817863300.0, 45452422.0, "C2 2 1.fq.gz", "0:150 1:150", "A:1964890519;C:1446826412;G:1428708103;T:1977297439;N:140827", 150, 150, null, null, 1964890519, 1446826412, 1428708103, 1977297439, 140827, "SRX14028689", "SRS11864776", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.93045, null, 0.17846, null, 0.69116, null, 0.48565, null, 150, null, 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