{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.platform = \"BGISEQ\" and tissue_curation = \"Whole Organism\"", "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. 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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. 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 3", null, "strain:danio rerio AgNPs2|breed:zebrafish9|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 3", "AG 2 3", "AG 2 3", "treatment6", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C2-3_1.fq.gz C2-3_2.fq.gz", "fastq fastq", 6782959200.0, 45219728.0, "C2 3 1.fq.gz", "0:150 1:150", "A:1949560199;C:1443524899;G:1428814233;T:1960921903;N:137966", 150, 150, null, null, 1949560199, 1443524899, 1428814233, 1960921903, 137966, "SRX14028690", "SRS11864777", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.93181, null, 0.17739, null, 0.6927, null, 0.50528, 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"], [67886, "SRR17868937", "SRX14028689", "SRS11864776", "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, "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, "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"], [67887, "SRR17868938", "SRX14028688", "SRS11864774", "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, "C2 1", null, "strain:danio rerio AgNPs2|breed:zebrafish7|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 1", "AG 2 1", "AG 2 1", "treatment4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C2-1_1.fq.gz C2-1_2.fq.gz", "fastq fastq", 6795911700.0, 45306078.0, "C2 1 1.fq.gz", "0:150 1:150", "A:1910936263;C:1486390531;G:1471463982;T:1927036309;N:84615", 150, 150, null, null, 1910936263, 1486390531, 1471463982, 1927036309, 84615, "SRX14028688", "SRS11864774", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.93638, null, 0.14847, null, 0.6814, null, 0.46864, 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"], [67888, "SRR17868939", "SRX14028687", "SRS11864775", "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, "C1 3", null, "strain:danio rerio AgNPs1|breed:zebrafish6|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 1 3", "AG 1 3", "AG 1 3", "treatment3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C1-3_1.fq.gz C1-3_2.fq.gz", "fastq fastq", 6788960100.0, 45259734.0, "C1 3 1.fq.gz", "0:150 1:150", "A:1883226902;C:1511814926;G:1492397960;T:1901504019;N:16293", 150, 150, null, null, 1883226902, 1511814926, 1492397960, 1901504019, 16293, "SRX14028687", "SRS11864775", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.94253, null, 0.12673, null, 0.67623, null, 0.49289, 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"], [67889, "SRR17868940", "SRX14028686", "SRS11864773", "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, "C1 2", null, "strain:danio rerio AgNPs1|breed:zebrafish5|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 1 2", "AG 1 2", "AG 1 2", "treatment2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C1-2_1.fq.gz C1-2_2.fq.gz", "fastq fastq", 6781043100.0, 45206954.0, "C1 2 1.fq.gz", "0:150 1:150", "A:1890710017;C:1500221789;G:1482973456;T:1907121929;N:15909", 150, 150, null, null, 1890710017, 1500221789, 1482973456, 1907121929, 15909, "SRX14028686", "SRS11864773", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.93834, null, 0.13288, null, 0.67777, null, 0.49269, 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"], [67890, "SRR17868941", "SRX14028685", "SRS11864772", "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, "C1 1", null, "strain:danio rerio AgNPs1|breed:zebrafish4|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 1 1", "AG 1 1", "AG 1 1", "treatment1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C1-1_1.fq.gz C1-1_2.fq.gz", "fastq fastq", 6760511100.0, 45070074.0, "C1 1 1.fq.gz", "0:150 1:150", "A:1875451292;C:1504527737;G:1489983693;T:1890505493;N:42885", 150, 150, null, null, 1875451292, 1504527737, 1489983693, 1890505493, 42885, "SRX14028685", "SRS11864772", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.94039, null, 0.1298, null, 0.68071, null, 0.49309, 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"], [67891, "SRR17868942", "SRX14028684", "SRS11864771", "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, "WT3", null, "strain:danio rerio con3|breed:zebrafish3|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 0 3", "WT 0 3", "WT 0 3", "control3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 6735369300.0, 44902462.0, "WT3 1.fq.gz", "0:150 1:150", "A:1853105410;C:1513363689;G:1496503080;T:1872187115;N:210006", 150, 150, null, null, 1853105410, 1513363689, 1496503080, 1872187115, 210006, "SRX14028684", "SRS11864771", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.94653, null, 0.11174, null, 0.69116, null, 0.49069, 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"], [67892, "SRR17868943", "SRX14028683", "SRS11864768", "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 3", null, "strain:danio rerio AgNPs4|breed:zebrafish12|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 3", "AG 4 3", "AG 4 3", "treatment9", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C4-3_1.fq.gz C4-3_2.fq.gz", "fastq fastq", 7066801800.0, 47112012.0, "C4 3 1.fq.gz", "0:150 1:150", "A:2079705050;C:1456973666;G:1436564156;T:2093467396;N:91532", 150, 150, null, null, 2079705050, 1456973666, 1436564156, 2093467396, 91532, "SRX14028683", "SRS11864768", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.92264, null, 0.21457, null, 0.70236, null, 0.52765, 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"], [67893, "SRR17868944", "SRX14028682", "SRS11864769", "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 2", null, "strain:danio rerio AgNPs4|breed:zebrafish11|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 2", "AG 4 2", "AG 4 2", "treatment8", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "C4-2_1.fq.gz C4-2_2.fq.gz", "fastq fastq", 6813742200.0, 45424948.0, "C4 2 1.fq.gz", "0:150 1:150", "A:1969847243;C:1438590202;G:1418612399;T:1986677730;N:14626", 150, 150, null, null, 1969847243, 1438590202, 1418612399, 1986677730, 14626, "SRX14028682", "SRS11864769", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.92909, null, 0.18109, null, 0.69029, null, 0.50538, 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"], [67894, "SRR17868945", "SRX14028681", "SRS11864770", "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, "WT2", null, "strain:danio rerio con2|breed:zebrafish2|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 0 2", "WT 0 2", "WT 0 2", "control2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 6760866900.0, 45072446.0, "WT2 1.fq.gz", "0:150 1:150", "A:1893259201;C:1485992528;G:1471666738;T:1909709705;N:238728", 150, 150, null, null, 1893259201, 1485992528, 1471666738, 1909709705, 238728, "SRX14028681", "SRS11864770", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.94132, null, 0.13956, null, 0.68596, null, 0.48309, 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"], [67895, "SRR17868946", "SRX14028680", "SRS11864767", "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, "WT1", null, "strain:danio rerio con1|breed:zebrafish1|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 0 1", "WT 0 1", "WT 0 1", "control1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP358022", null, null, "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 7003449300.0, 46689662.0, "WT1 1.fq.gz", "0:150 1:150", "A:1946491315;C:1554368011;G:1539879203;T:1962458586;N:252185", 150, 150, null, null, 1946491315, 1554368011, 1539879203, 1962458586, 252185, "SRX14028680", "SRS11864767", "SRA1350965", "Center for Neuroscience|Shantou university", "Center for Neuroscience", 1, 0.94236, null, 0.12627, null, 0.68369, null, 0.49408, 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"], [68195, "SRR17658724", "SRX13826757", "SRS11705915", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C25d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:25dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C25D", "C25D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20541691800.0, 68472306.0, "C25D.7z", "0:150 1:150", "A:5668751376;C:4596699177;G:4545478495;T:5730382931;N:379821", 150, 150, null, null, 5668751376, 4596699177, 4545478495, 5730382931, 379821, "SRX13826757", "SRS11705915", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.84223, 0.84372, 0.07155, 0.07222, 0.70189, 0.70321, 0.47909, 0.495, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-07", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [68196, "SRR17658725", "SRX13826756", "SRS11705914", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "T60d  ZHT", null, "strain:AB|isolate:35|breed:zebrafish|cultivar:TEST|ecotype:CHINA|age:60dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "T60D", "T60D", "heat treated zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20334742200.0, 67782474.0, "T60D.7z", "0:150 1:150", "A:5482201207;C:4682998764;G:4635775004;T:5533378494;N:388731", 150, 150, null, null, 5482201207, 4682998764, 4635775004, 5533378494, 388731, "SRX13826756", "SRS11705914", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.94378, 0.94515, 0.04989, 0.04997, 0.69848, 0.69978, 0.50317, 0.5041, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68197, "SRR17658726", "SRX13826755", "SRS11705913", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "T45d  ZHT", null, "strain:AB|isolate:35|breed:zebrafish|cultivar:TEST|ecotype:CHINA|age:45dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "T45D", "T45D", "heat treated zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20230560300.0, 67435201.0, "T45D.7z", "0:150 1:150", "A:5444816209;C:4663007584;G:4631943733;T:5490408754;N:384020", 150, 150, null, null, 5444816209, 4663007584, 4631943733, 5490408754, 384020, "SRX13826755", "SRS11705913", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.88041, 0.881, 0.04485, 0.04492, 0.72163, 0.72236, 0.52232, 0.52307, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68198, "SRR17658727", "SRX13826754", "SRS11705912", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "T35d  ZHT", null, "strain:AB|isolate:35|breed:zebrafish|cultivar:TEST|ecotype:CHINA|age:35dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "T35D", "T35D", "heat treated zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20630503200.0, 68768344.0, "T35D.7z", "0:150 1:150", "A:5660657832;C:4654929757;G:4598083304;T:5716350276;N:482031", 150, 150, null, null, 5660657832, 4654929757, 4598083304, 5716350276, 482031, "SRX13826754", "SRS11705912", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.9134, 0.91476, 0.06961, 0.06972, 0.69035, 0.69215, 0.52155, 0.5154, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68199, "SRR17658728", "SRX13826753", "SRS11705911", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C60d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:60dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C60D", "C60D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 10921407600.0, 44923977.0, "C60D.7z", null, "A:2992232295;C:2470688717;G:2440861228;T:3017432565;N:192795", null, null, null, null, 2992232295, 2470688717, 2440861228, 3017432565, 192795, "SRX13826753", "SRS11705911", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.93932, 0.94095, 0.06489, 0.06559, 0.77871, 0.77759, 0.56384, 0.56447, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68200, "SRR17658729", "SRX13826752", "SRS11705910", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C45d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:45dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C45D", "C45D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20413229700.0, 68044099.0, "C45D.7z", "0:150 1:150", "A:5619395833;C:4581611789;G:4543973618;T:5667873613;N:374847", 150, 150, null, null, 5619395833, 4581611789, 4543973618, 5667873613, 374847, "SRX13826752", "SRS11705910", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.86848, 0.87064, 0.0719, 0.07252, 0.69879, 0.69834, 0.52279, 0.51074, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [68201, "SRR17658730", "SRX13826751", "SRS11705909", "SRP355720", "PRJNA798511", "Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation", "PRJNA798511", "Other", "heat treated zebrafish", null, null, null, null, "C35d  ZHT", null, "strain:AB|isolate:28|breed:zebrafish|cultivar:WT|ecotype:CHINA|age:35dpf|sex:not collected|tissue:whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAq of zebrafish", "C35D", "C35D", "WT zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP355720", null, "loader:fastq load.py", null, null, 20469803700.0, 68232679.0, "C35D.7z", "0:150 1:150", "A:5556774511;C:4678377106;G:4627472920;T:5606765895;N:413268", 150, 150, null, null, 5556774511, 4678377106, 4627472920, 5606765895, 413268, "SRX13826751", "SRS11705909", "SRA1358616", "Hunan University of Science and Technology|School of Life and Health Sciences", "Hunan University of Science and Technology", 2, 0.93663, 0.93871, 0.06853, 0.06895, 0.6982, 0.69901, 0.51209, 0.51148, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-09", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69610, "SRR18959644", "SRX15036823", "SRS12783659", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 3", "GSM6070558", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070558", "GSM6070558: T60d 3; Danio rerio; RNA Seq", "GSM6070558 r1", "GSM6070558", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_3_1.fq.gz T60d_3_2.fq.gz", "fastq fastq", 6668586300.0, 44457242.0, "GSM6070558 r1", "0:150 1:150", "A:1798105768;C:1533776293;G:1519933345;T:1816635529;N:135365", 150, 150, null, null, 1798105768, 1533776293, 1519933345, 1816635529, 135365, "SRX15036823", "SRS12783659", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94696, null, 0.03818, null, 0.72754, null, 0.44424, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69611, "SRR18959645", "SRX15036822", "SRS12783660", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 2", "GSM6070557", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070557", "GSM6070557: T60d 2; Danio rerio; RNA Seq", "GSM6070557 r1", "GSM6070557", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_2_1.fq.gz T60d_2_2.fq.gz", "fastq fastq", 6790474800.0, 45269832.0, "GSM6070557 r1", "0:150 1:150", "A:1792022273;C:1601949824;G:1583360851;T:1813022005;N:119847", 150, 150, null, null, 1792022273, 1601949824, 1583360851, 1813022005, 119847, "SRX15036822", "SRS12783660", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9518, null, 0.03662, null, 0.72892, null, 0.50564, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69612, "SRR18959646", "SRX15036821", "SRS12783661", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T60d 1", "GSM6070556", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "T60d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:heat shock", "GSM6070556", "GSM6070556: T60d 1; Danio rerio; RNA Seq", "GSM6070556 r1", "GSM6070556", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T60d_1_1.fq.gz T60d_1_2.fq.gz", "fastq fastq", 6875681100.0, 45837874.0, "GSM6070556 r1", "0:150 1:150", "A:1892073166;C:1547272647;G:1532480808;T:1903720960;N:133519", 150, 150, null, null, 1892073166, 1547272647, 1532480808, 1903720960, 133519, "SRX15036821", "SRS12783661", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93516, null, 0.0737, null, 0.70394, null, 0.55661, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69613, "SRR18959647", "SRX15036820", "SRS12783658", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 3", "GSM6070555", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070555", "GSM6070555: T45d 3; Danio rerio; RNA Seq", "GSM6070555 r1", "GSM6070555", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_3_1.fq.gz T45d_3_2.fq.gz", "fastq fastq", 6677602800.0, 44517352.0, "GSM6070555 r1", "0:150 1:150", "A:1776927020;C:1564627916;G:1551750199;T:1784113081;N:184584", 150, 150, null, null, 1776927020, 1564627916, 1551750199, 1784113081, 184584, "SRX15036820", "SRS12783658", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.95333, null, 0.04626, null, 0.79788, null, 0.53869, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69614, "SRR18959648", "SRX15036819", "SRS12783657", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 2", "GSM6070554", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070554", "GSM6070554: T45d 2; Danio rerio; RNA Seq", "GSM6070554 r1", "GSM6070554", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_2_1.fq.gz T45d_2_2.fq.gz", "fastq fastq", 6866885100.0, 45779234.0, "GSM6070554 r1", "0:150 1:150", "A:1855996561;C:1572989256;G:1559095064;T:1878636946;N:167273", 150, 150, null, null, 1855996561, 1572989256, 1559095064, 1878636946, 167273, "SRX15036819", "SRS12783657", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.85691, null, 0.0428, null, 0.70059, null, 0.48517, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69615, "SRR18959649", "SRX15036818", "SRS12783655", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T45d 1", "GSM6070553", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "T45d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:heat shock", "GSM6070553", "GSM6070553: T45d 1; Danio rerio; RNA Seq", "GSM6070553 r1", "GSM6070553", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T45d_1_1.fq.gz T45d_1_2.fq.gz", "fastq fastq", 6686072400.0, 44573816.0, "GSM6070553 r1", "0:150 1:150", "A:1811892628;C:1525390412;G:1521098470;T:1827658727;N:32163", 150, 150, null, null, 1811892628, 1525390412, 1521098470, 1827658727, 32163, "SRX15036818", "SRS12783655", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.83063, null, 0.04482, null, 0.75227, null, 0.53268, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69616, "SRR18959650", "SRX15036817", "SRS12783656", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 3", "GSM6070552", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070552", "GSM6070552: T35d 3; Danio rerio; RNA Seq", "GSM6070552 r1", "GSM6070552", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_3_1.fq.gz T35d_3_2.fq.gz", "fastq fastq", 6886247700.0, 45908318.0, "GSM6070552 r1", "0:150 1:150", "A:1822190170;C:1616493163;G:1597658988;T:1849741504;N:163875", 150, 150, null, null, 1822190170, 1616493163, 1597658988, 1849741504, 163875, "SRX15036817", "SRS12783656", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94299, null, 0.03719, null, 0.71165, null, 0.49413, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69617, "SRR18959651", "SRX15036816", "SRS12783654", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 2", "GSM6070551", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070551", "GSM6070551: T35d 2; Danio rerio; RNA Seq", "GSM6070551 r1", "GSM6070551", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_2_1.fq.gz T35d_2_2.fq.gz", "fastq fastq", 6851241900.0, 45674946.0, "GSM6070551 r1", "0:150 1:150", "A:1925245234;C:1503184374;G:1483632128;T:1939009289;N:170875", 150, 150, null, null, 1925245234, 1503184374, 1483632128, 1939009289, 170875, "SRX15036816", "SRS12783654", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.86703, null, 0.08277, null, 0.70619, null, 0.47871, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69618, "SRR18959652", "SRX15036815", "SRS12783653", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "T35d 1", "GSM6070550", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "T35d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:heat shock", "GSM6070550", "GSM6070550: T35d 1; Danio rerio; RNA Seq", "GSM6070550 r1", "GSM6070550", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "T35d_1_1.fq.gz T35d_1_2.fq.gz", "fastq fastq", 6893013600.0, 45953424.0, "GSM6070550 r1", "0:150 1:150", "A:1913222428;C:1535252220;G:1516792188;T:1927599483;N:147281", 150, 150, null, null, 1913222428, 1535252220, 1516792188, 1927599483, 147281, "SRX15036815", "SRS12783653", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93126, null, 0.08861, null, 0.70711, null, 0.53182, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69619, "SRR18959653", "SRX15036814", "SRS12783652", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 3", "GSM6070549", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070549", "GSM6070549: C60d 3; Danio rerio; RNA Seq", "GSM6070549 r1", "GSM6070549", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_3_1.fq.gz C60d_3_2.fq.gz", "fastq fastq", 6732458700.0, 44883058.0, "GSM6070549 r1", "0:150 1:150", "A:1840891044;C:1527037740;G:1515664962;T:1848770869;N:94085", 150, 150, null, null, 1840891044, 1527037740, 1515664962, 1848770869, 94085, "SRX15036814", "SRS12783652", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94478, null, 0.05996, null, 0.73661, null, 0.56885, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69620, "SRR18959654", "SRX15036813", "SRS12783651", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 2", "GSM6070548", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070548", "GSM6070548: C60d 2; Danio rerio; RNA Seq", "GSM6070548 r1", "GSM6070548", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_2_1.fq.gz C60d_2_2.fq.gz", "fastq fastq", 6920478600.0, 46136524.0, "GSM6070548 r1", "0:150 1:150", "A:1860288879;C:1602876302;G:1589399217;T:1867783032;N:131170", 150, 150, null, null, 1860288879, 1602876302, 1589399217, 1867783032, 131170, "SRX15036813", "SRS12783651", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.95235, null, 0.05236, null, 0.74836, null, 0.55427, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69621, "SRR18959655", "SRX15036812", "SRS12783650", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C60d 1", "GSM6070547", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "C60d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:60dpf|treatment:control", "GSM6070547", "GSM6070547: C60d 1; Danio rerio; RNA Seq", "GSM6070547 r1", "GSM6070547", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C60d_1_1.fq.gz C60d_1_2.fq.gz", "fastq fastq", 6744639300.0, 44964262.0, "GSM6070547 r1", "0:150 1:150", "A:1855599360;C:1516548729;G:1501772747;T:1870587619;N:130845", 150, 150, null, null, 1855599360, 1516548729, 1501772747, 1870587619, 130845, "SRX15036812", "SRS12783650", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.93949, null, 0.06857, null, 0.73805, null, 0.54443, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69622, "SRR18959656", "SRX15036811", "SRS12783649", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 3", "GSM6070546", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070546", "GSM6070546: C45d 3; Danio rerio; RNA Seq", "GSM6070546 r1", "GSM6070546", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_3_1.fq.gz C45d_3_2.fq.gz", "fastq fastq", 6743568300.0, 44957122.0, "GSM6070546 r1", "0:150 1:150", "A:1852733188;C:1516814321;G:1505754587;T:1868137549;N:128655", 150, 150, null, null, 1852733188, 1516814321, 1505754587, 1868137549, 128655, "SRX15036811", "SRS12783649", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.87046, null, 0.07264, null, 0.69996, null, 0.51275, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69623, "SRR18959657", "SRX15036810", "SRS12783648", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 2", "GSM6070545", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070545", "GSM6070545: C45d 2; Danio rerio; RNA Seq", "GSM6070545 r1", "GSM6070545", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_2_1.fq.gz C45d_2_2.fq.gz", "fastq fastq", 6742016100.0, 44946774.0, "GSM6070545 r1", "0:150 1:150", "A:1859613225;C:1508260261;G:1496299109;T:1877718155;N:125350", 150, 150, null, null, 1859613225, 1508260261, 1496299109, 1877718155, 125350, "SRX15036810", "SRS12783648", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.84381, null, 0.07253, null, 0.68769, null, 0.51224, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69624, "SRR18959658", "SRX15036809", "SRS12783647", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C45d 1", "GSM6070544", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "C45d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:45dpf|treatment:control", "GSM6070544", "GSM6070544: C45d 1; Danio rerio; RNA Seq", "GSM6070544 r1", "GSM6070544", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C45d_1_1.fq.gz C45d_1_2.fq.gz", "fastq fastq", 6927645300.0, 46184302.0, "GSM6070544 r1", "0:150 1:150", "A:1907049420;C:1556537207;G:1541919922;T:1922017909;N:120842", 150, 150, null, null, 1907049420, 1556537207, 1541919922, 1922017909, 120842, "SRX15036809", "SRS12783647", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.89529, null, 0.07244, null, 0.71703, null, 0.53737, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69625, "SRR18959659", "SRX15036808", "SRS12783646", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 3", "GSM6070543", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070543", "GSM6070543: C35d 3; Danio rerio; RNA Seq", "GSM6070543 r1", "GSM6070543", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_3_1.fq.gz C35d_3_2.fq.gz", "fastq fastq", 6874832400.0, 45832216.0, "GSM6070543 r1", "0:150 1:150", "A:1849406781;C:1586828671;G:1570455371;T:1867999362;N:142215", 150, 150, null, null, 1849406781, 1586828671, 1570455371, 1867999362, 142215, "SRX15036808", "SRS12783646", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.94372, null, 0.06412, null, 0.71043, null, 0.5035, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69626, "SRR18959660", "SRX15036807", "SRS12783645", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 2", "GSM6070542", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 2", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070542", "GSM6070542: C35d 2; Danio rerio; RNA Seq", "GSM6070542 r1", "GSM6070542", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_2_1.fq.gz C35d_2_2.fq.gz", "fastq fastq", 6709504200.0, 44730028.0, "GSM6070542 r1", "0:150 1:150", "A:1832012065;C:1521825928;G:1505192413;T:1850347840;N:125954", 150, 150, null, null, 1832012065, 1521825928, 1505192413, 1850347840, 125954, "SRX15036807", "SRS12783645", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9254, null, 0.07577, null, 0.67537, null, 0.51805, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69627, "SRR18959661", "SRX15036806", "SRS12783644", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C35d 1", "GSM6070541", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "C35d 1", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:35dpf|treatment:control", "GSM6070541", "GSM6070541: C35d 1; Danio rerio; RNA Seq", "GSM6070541 r1", "GSM6070541", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C35d_1_1.fq.gz C35d_1_2.fq.gz", "fastq fastq", 6885467100.0, 45903114.0, "GSM6070541 r1", "0:150 1:150", "A:1875355665;C:1569722507;G:1551825136;T:1888418693;N:145099", 150, 150, null, null, 1875355665, 1569722507, 1551825136, 1888418693, 145099, "SRX15036806", "SRS12783644", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 0.9444, null, 0.06579, null, 0.73312, null, 0.53564, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-27", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [69628, "SRR18959662", "SRX15036805", "SRS12783643", "SRP372606", "PRJNA832865", "Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation", "GSE201748", "Transcriptome Analysis", "The influence of environmental factors  especially temperature  on sex ratio is of great significance to elucidate the mechanism of sex determination. However  the molecular mechanisms by which temperature affects sex determination remains unclear  although a few candidate genes have been found to play a role in the process. In this study  we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171  1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35  45 dpf and 60 dpf dpf respectively  revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway  cell cycle  oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization  and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation", null, "pubmed:35641933", null, "C25d 3", "GSM6070540", null, "source name:Whole fish|tissue:Whole fish|strain:AB|genotype:Wide type|development stage:25dpf|treatment:control", "C25d 3", "The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base\u2018N\u2019 base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11  then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value \u2264 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value\u2264 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample", "Whole fish", "The control group was kept at 28\u2103  whereas the thermal treatment group was exposed to 35\u2103for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment  fish were returned at 28\u2103 until the fish reached to sexual maturity 90 dpf.", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", "The AB strain were maintained in a glass aquarium with a circulating water system at 28\u00b10.5\u2103  with photoperiods of 14L 10D  and the number of fish in each 5 liter tank was 50 55.", "tissue:Whole fish|strain:AB|genotype:Wide type|development stage:25dpf|treatment:control", "GSM6070540", "GSM6070540: C25d 3; Danio rerio; RNA Seq", "GSM6070540 r1", "GSM6070540", "1", "Total RNA was extracted from the tissues using Trizol Invitrogen  Carlsbad  CA  USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube  followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4\u2103  then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s  and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation  the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol  then centrifuged at 13 600 rpm for 20 minutes at 4\u2103. post deserting the supernatant  the RNA pellet was washed twice with 1 mL 75% ethanol  then the mix was centrifuged at 13 600 rpm for 3 minutes at 4\u2103 to collect residual ethanol  followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally  25\u03bcL100\u03bcL of DEPC treated water was added to dissolve the RNA. Subsequently  total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific  MA  USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription  followed by a second strand cDNA synthesis. postwards  A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR  and products were purified by Ampure XP Beads  then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular  DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP372606", null, null, "C25d_3_1.fq.gz C25d_3_2.fq.gz", "fastq fastq", 6919024500.0, 46126830.0, "GSM6070540 r1", "0:150 1:150", "A:1895872624;C:1561159730;G:1542389546;T:1919479874;N:122726", 150, 150, null, null, 1895872624, 1561159730, 1542389546, 1919479874, 122726, "SRX15036805", "SRS12783643", "SRA1411536", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", "Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology", 1, 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