{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Multi-stage\" and tissue_curation = \"Brain\"", "rows": [[29047, "SRR26990800", "SRX22683819", "SRS19677533", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "WT brain 3", "GSM7924152", null, "source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT brain 3", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "brain", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:wildtype|time:50dpf", "GSM7924152", "GSM7924152: WT brain 3; Danio rerio; RNA Seq", "GSM7924152 r1", "GSM7924152", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "6_WT_3B_S21_L001_R2_001.fastq.gz 6_WT_3B_S21_L001_R1_001.fastq.gz", "fastq fastq", 4461174200.0, 14772100.0, "GSM7924152 r1", "0:151 1:151", "A:1278513355;C:956242646;G:972856171;T:1253520960;N:41068", 151, 151, null, null, 1278513355, 956242646, 972856171, 1253520960, 41068, "SRX22683819", "SRS19677533", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93808, 0.93817, 0.14984, 0.14408, 0.70388, 0.7035, 0.49899, 0.49333, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29048, "SRR26990801", "SRX22683818", "SRS19677532", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "WT brain 2", "GSM7924151", null, "source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT brain 2", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "brain", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:wildtype|time:50dpf", "GSM7924151", "GSM7924151: WT brain 2; Danio rerio; RNA Seq", "GSM7924151 r1", "GSM7924151", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "5_WT_2B_S20_L001_R2_001.fastq.gz 5_WT_2B_S20_L001_R1_001.fastq.gz", "fastq fastq", 4801957946.0, 15900523.0, "GSM7924151 r1", "0:151 1:151", "A:1362644269;C:1038749357;G:1059777543;T:1340744881;N:41896", 151, 151, null, null, 1362644269, 1038749357, 1059777543, 1340744881, 41896, "SRX22683818", "SRS19677532", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.9395, 0.94022, 0.14136, 0.13794, 0.70853, 0.70845, 0.48158, 0.51366, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29049, "SRR26990802", "SRX22683817", "SRS19677531", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "WT brain 1", "GSM7924150", null, "source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT brain 1", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "brain", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:wildtype|time:50dpf", "GSM7924150", "GSM7924150: WT brain 1; Danio rerio; RNA Seq", "GSM7924150 r1", "GSM7924150", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "4_WT_1B_S19_L001_R1_001.fastq.gz 4_WT_1B_S19_L001_R2_001.fastq.gz", "fastq fastq", 1712568916.0, 5670758.0, "GSM7924150 r1", "0:151 1:151", "A:496576572;C:361494257;G:367701092;T:486774148;N:22847", 151, 151, null, null, 496576572, 361494257, 367701092, 486774148, 22847, "SRX22683817", "SRS19677531", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.92654, 0.92757, 0.14818, 0.14172, 0.71394, 0.7122, 0.5011, 0.50084, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29050, "SRR26990803", "SRX22683816", "SRS19677530", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "itgavKO brain 3", "GSM7924149", null, "source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO brain 3", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "brain", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:itgavKO mutant|time:50dpf", "GSM7924149", "GSM7924149: itgavKO brain 3; Danio rerio; RNA Seq", "GSM7924149 r1", "GSM7924149", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "3_itgavKO_3B_S18_L001_R2_001.fastq.gz 3_itgavKO_3B_S18_L001_R1_001.fastq.gz", "fastq fastq", 3079420614.0, 10196757.0, "GSM7924149 r1", "0:151 1:151", "A:869781292;C:673463468;G:684386550;T:851761331;N:27973", 151, 151, null, null, 869781292, 673463468, 684386550, 851761331, 27973, "SRX22683816", "SRS19677530", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.94057, 0.94157, 0.13371, 0.12847, 0.70429, 0.70451, 0.49726, 0.49861, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29051, "SRR26990804", "SRX22683815", "SRS19677529", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "itgavKO brain 2", "GSM7924148", null, "source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO brain 2", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "brain", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:itgavKO mutant|time:50dpf", "GSM7924148", "GSM7924148: itgavKO brain 2; Danio rerio; RNA Seq", "GSM7924148 r1", "GSM7924148", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "2_itgavKO_2B_S17_L001_R1_001.fastq.gz 2_itgavKO_2B_S17_L001_R2_001.fastq.gz", "fastq fastq", 1913701218.0, 6336759.0, "GSM7924148 r1", "0:151 1:151", "A:549324781;C:410519448;G:417112515;T:536726028;N:18446", 151, 151, null, null, 549324781, 410519448, 417112515, 536726028, 18446, "SRX22683815", "SRS19677529", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93075, 0.93209, 0.15174, 0.14613, 0.70449, 0.70475, 0.48199, 0.48317, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29052, "SRR26990805", "SRX22683814", "SRS19677528", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF \u00df signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.", null, "pubmed:39526957", null, "itgavKO brain 1", "GSM7924147", null, "source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO brain 1", "The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.", "brain", "Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", "For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5\u00b0C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:itgavKO mutant|time:50dpf", "GSM7924147", "GSM7924147: itgavKO brain 1; Danio rerio; RNA Seq", "GSM7924147 r1", "GSM7924147", "1", "RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "1_itgavKO_1B_S16_L001_R1_001.fastq.gz 1_itgavKO_1B_S16_L001_R2_001.fastq.gz", "fastq fastq", 2056389876.0, 6809238.0, "GSM7924147 r1", "0:151 1:151", "A:593258034;C:437927433;G:446814957;T:578370581;N:18871", 151, 151, null, null, 593258034, 437927433, 446814957, 578370581, 18871, "SRX22683814", "SRS19677528", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93156, 0.93304, 0.1488, 0.14352, 0.70224, 0.70293, 0.49609, 0.49296, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29059, "SRR27010032", "SRX22702842", "SRS19695451", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C3", "C3", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C3", "C3", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C3_R2_001.fastq.gz C3_R1_001.fastq.gz", "fastq fastq", 7226125500.0, 24087085.0, "C3 R1 001.fastq.gz", "0:150 1:150", "A:1960622478;C:1648410555;G:1694156766;T:1922924543;N:11158", 150, 150, null, null, 1960622478, 1648410555, 1694156766, 1922924543, 11158, "SRX22702842", "SRS19695451", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94281, 0.94259, 0.11548, 0.11243, 0.666, 0.66768, 0.4931, 0.49197, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29060, "SRR27010033", "SRX22702841", "SRS19695450", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C2", "C2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C2", "C2", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C2_R1_001.fastq.gz C2_R2_001.fastq.gz", "fastq fastq", 5174981700.0, 17249939.0, "C2 R1 001.fastq.gz", "0:150 1:150", "A:1397754308;C:1184093732;G:1220417954;T:1372707855;N:7851", 150, 150, null, null, 1397754308, 1184093732, 1220417954, 1372707855, 7851, "SRX22702841", "SRS19695450", "SRA1760882", "University of 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null, null, null, null, "RNA seq of zebrafish: brain", "B6", "B6", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B6_R1_001.fastq.gz B6_R2_001.fastq.gz", "fastq fastq", 6038798100.0, 20129327.0, "B6 R1 001.fastq.gz", "0:150 1:150", "A:1644314055;C:1369774666;G:1410590989;T:1614109292;N:9098", 150, 150, null, null, 1644314055, 1369774666, 1410590989, 1614109292, 9098, "SRX22702840", "SRS19695449", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94338, 0.9424, 0.12398, 0.12103, 0.69075, 0.69203, 0.49627, 0.49707, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29062, "SRR27010035", "SRX22702839", "SRS19695448", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT irf8 sham B4", "B4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B4", "B4", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B4_R1_001.fastq.gz 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null, "WT irf8 sham B3", "B3", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B3", "B3", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B3_R1_001.fastq.gz B3_R2_001.fastq.gz", "fastq fastq", 5982538500.0, 19941795.0, "B3 R1 001.fastq.gz", "0:150 1:150", "A:1606272011;C:1379162914;G:1419047430;T:1578047050;N:9095", 150, 150, null, null, 1606272011, 1379162914, 1419047430, 1578047050, 9095, "SRX22702838", "SRS19695446", "SRA1760882", "University of York|Biology", "University of York", 2, 0.95017, 0.9501, 0.09939, 0.09688, 0.68838, 0.68964, 0.48756, 0.49223, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29064, "SRR27010037", "SRX22702837", "SRS19695447", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT irf8 sham B2", "B2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B2", "B2", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B2_R2_001.fastq.gz B2_R1_001.fastq.gz", "fastq fastq", 5653227300.0, 18844091.0, "B2 R1 001.fastq.gz", "0:150 1:150", "A:1525579353;C:1295599509;G:1332714404;T:1499325712;N:8322", 150, 150, null, null, 1525579353, 1295599509, 1332714404, 1499325712, 8322, "SRX22702837", "SRS19695447", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94379, 0.89488, 0.12085, 0.10989, 0.69004, 0.69796, 0.48877, 0.48916, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29065, "SRR27010038", "SRX22702836", "SRS19695445", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT scr sham A9", "A9", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A9", "A9", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A9_R1_001.fastq.gz A9_R2_001.fastq.gz", "fastq fastq", 5280286800.0, 17600956.0, "A9 R1 001.fastq.gz", "0:150 1:150", "A:1438789477;C:1200820278;G:1228527888;T:1412141110;N:8047", 150, 150, null, null, 1438789477, 1200820278, 1228527888, 1412141110, 8047, "SRX22702836", "SRS19695445", "SRA1760882", "University of York|Biology", "University of York", 2, 0.93991, 0.93997, 0.12415, 0.11988, 0.68043, 0.68245, 0.49031, 0.49263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29066, "SRR27010039", "SRX22702835", "SRS19695444", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G8", "G8", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G8", "G8", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G8_R1_001.fastq.gz G8_R2_001.fastq.gz", "fastq fastq", 6258269400.0, 20860898.0, "G8 R1 001.fastq.gz", "0:150 1:150", "A:1703536007;C:1424705894;G:1461517358;T:1668500971;N:9170", 150, 150, null, null, 1703536007, 1424705894, 1461517358, 1668500971, 9170, "SRX22702835", "SRS19695444", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94463, 0.94425, 0.12179, 0.11924, 0.68383, 0.68574, 0.48927, 0.49078, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29067, "SRR27010040", "SRX22702834", "SRS19695443", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G5", "G5", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: 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"SRS19695442", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G4", "G4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G4", "G4", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G4_R2_001.fastq.gz 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null, null, "rnaset2 irf8 transplanted visible cells G1", "G1", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G1", "G1", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G1_R1_001.fastq.gz G1_R2_001.fastq.gz", "fastq fastq", 6745303500.0, 22484345.0, "G1 R1 001.fastq.gz", "0:150 1:150", "A:1832990297;C:1535916761;G:1572331210;T:1804054965;N:10267", 150, 150, null, null, 1832990297, 1535916761, 1572331210, 1804054965, 10267, "SRX22702832", "SRS19695441", "SRA1760882", "University of York|Biology", "University 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"SRR27010056", "SRX22702818", "SRS19695427", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C4", "C4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C4", "C4", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C4_R1_001.fastq.gz 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null, null, "WT scr sham A2", "A2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A2", "A2", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A2_R1_001.fastq.gz A2_R2_001.fastq.gz", "fastq fastq", 9528853800.0, 31762846.0, "A2 R1 001.fastq.gz", "0:150 1:150", "A:2597197507;C:2160049241;G:2216864264;T:2554728048;N:14740", 150, 150, null, null, 2597197507, 2160049241, 2216864264, 2554728048, 14740, "SRX22702817", "SRS19695425", "SRA1760882", "University of York|Biology", "University of York", 2, 0.9445, 0.94377, 0.12789, 0.12443, 0.68414, 0.68456, 0.48493, 0.49203, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29085, "SRR27010058", "SRX22702816", "SRS19695426", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT scr sham A1", "A1", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A1", "A1", "RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A1_R1_001.fastq.gz A1_R2_001.fastq.gz", "fastq fastq", 7478013000.0, 24926710.0, "A1 R1 001.fastq.gz", "0:150 1:150", "A:2052485809;C:1681219485;G:1732402686;T:2011893634;N:11386", 150, 150, null, null, 2052485809, 1681219485, 1732402686, 2011893634, 11386, "SRX22702816", "SRS19695426", "SRA1760882", "University of York|Biology", "University of York", 2, 0.9395, 0.93867, 0.13153, 0.12753, 0.68933, 0.691, 0.4882, 0.48774, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29820, "SRR27499202", "SRX23170207", "SRS20119604", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 19 1", "GSM8012748", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 19 1", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012748", "GSM8012748: non syn 19 1; Danio rerio; RNA Seq", "GSM8012748 r1", "GSM8012748", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-19-1_extract_R1.fastq non-syn-19-1_extract_R2.fastq", "fastq fastq", 3117719100.0, 10392397.0, "GSM8012748 r1", "0:150 1:150", "A:895917474;C:489293250;G:641228744;T:1091230120;N:49512", 150, 150, null, null, 895917474, 489293250, 641228744, 1091230120, 49512, "SRX23170207", "SRS20119604", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29821, "SRR27499203", "SRX23170206", "SRS20119603", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 10 1", "GSM8012747", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 10 1", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012747", "GSM8012747: non syn 10 1; Danio rerio; RNA Seq", "GSM8012747 r1", "GSM8012747", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-10-1_S16_L003_R1_001.fastq.gz non-syn-10-1_S16_L003_R2_001.fastq.gz", "fastq fastq", 4498404600.0, 14994682.0, "GSM8012747 r1", "0:150 1:150", "A:1317989544;C:684597236;G:860222705;T:1635432063;N:163052", 150, 150, null, null, 1317989544, 684597236, 860222705, 1635432063, 163052, "SRX23170206", "SRS20119603", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29822, "SRR27499204", "SRX23170205", "SRS20119602", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 22", "GSM8012746", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 22", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012746", "GSM8012746: non syn 22; Danio rerio; RNA Seq", "GSM8012746 r1", "GSM8012746", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-22_S1_L001_R1_001.fastq.gz non-syn-22_S1_L001_R2_001.fastq.gz", "fastq fastq", 2450883300.0, 8169611.0, "GSM8012746 r1", "0:150 1:150", "A:717072489;C:371259220;G:487966761;T:874532663;N:52167", 150, 150, null, null, 717072489, 371259220, 487966761, 874532663, 52167, "SRX23170205", "SRS20119602", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29823, "SRR27499205", "SRX23170204", "SRS20119601", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 18", "GSM8012745", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 18", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012745", "GSM8012745: non syn 18; Danio rerio; RNA Seq", "GSM8012745 r1", "GSM8012745", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-18_S1_L001_R1_001.fastq.gz non-syn-18_S1_L001_R2_001.fastq.gz", "fastq fastq", 2481275400.0, 8270918.0, "GSM8012745 r1", "0:150 1:150", "A:707890019;C:383065085;G:518277437;T:872001065;N:41794", 150, 150, null, null, 707890019, 383065085, 518277437, 872001065, 41794, "SRX23170204", "SRS20119601", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29824, "SRR27499206", "SRX23170203", "SRS20119600", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 17", "GSM8012744", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 17", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012744", "GSM8012744: non syn 17; Danio rerio; RNA Seq", "GSM8012744 r1", "GSM8012744", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-17_S1_L001_R1_001.fastq.gz non-syn-17_S1_L001_R2_001.fastq.gz", "fastq fastq", 1902575700.0, 6341919.0, "GSM8012744 r1", "0:150 1:150", "A:523356732;C:311424242;G:413587608;T:654191534;N:15584", 150, 150, null, null, 523356732, 311424242, 413587608, 654191534, 15584, "SRX23170203", "SRS20119600", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29825, "SRR27499207", "SRX23170202", "SRS20119599", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 15", "GSM8012743", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 15", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012743", "GSM8012743: non syn 15; Danio rerio; RNA Seq", "GSM8012743 r1", "GSM8012743", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-15_S1_L001_R1_001.fastq.gz non-syn-15_S1_L001_R2_001.fastq.gz", "fastq fastq", 2644568100.0, 8815227.0, "GSM8012743 r1", "0:150 1:150", "A:764042895;C:415507565;G:493804628;T:971168170;N:44842", 150, 150, null, null, 764042895, 415507565, 493804628, 971168170, 44842, "SRX23170202", "SRS20119599", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29826, "SRR27499208", "SRX23170201", "SRS20119598", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 13", "GSM8012742", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 13", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012742", "GSM8012742: non syn 13; Danio rerio; RNA Seq", "GSM8012742 r1", "GSM8012742", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-13_S1_L001_R1_001.fastq.gz non-syn-13_S1_L001_R2_001.fastq.gz", "fastq fastq", 3344411400.0, 11148038.0, "GSM8012742 r1", "0:150 1:150", "A:981997806;C:535742678;G:672084090;T:1154576135;N:10691", 150, 150, null, null, 981997806, 535742678, 672084090, 1154576135, 10691, "SRX23170201", "SRS20119598", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29827, "SRR27499209", "SRX23170200", "SRS20119597", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 10", "GSM8012741", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 10", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012741", "GSM8012741: non syn 10; Danio rerio; RNA Seq", "GSM8012741 r1", "GSM8012741", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-10_S17_L003_R1_001.fastq.gz non-syn-10_S17_L003_R2_001.fastq.gz", "fastq fastq", 4980891600.0, 16602972.0, "GSM8012741 r1", "0:150 1:150", "A:1442162587;C:766015788;G:971257296;T:1801275462;N:180467", 150, 150, null, null, 1442162587, 766015788, 971257296, 1801275462, 180467, "SRX23170200", "SRS20119597", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29828, "SRR27499210", "SRX23170199", "SRS20119596", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 6", "GSM8012740", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 6", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012740", "GSM8012740: non syn 6; Danio rerio; RNA Seq", "GSM8012740 r1", "GSM8012740", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-6_S1_L001_R1_001.fastq.gz non-syn-6_S1_L001_R2_001.fastq.gz", "fastq fastq", 3386439600.0, 11288132.0, "GSM8012740 r1", "0:150 1:150", "A:971399150;C:550458386;G:698401196;T:1166169792;N:11076", 150, 150, null, null, 971399150, 550458386, 698401196, 1166169792, 11076, "SRX23170199", "SRS20119596", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29829, "SRR27499211", "SRX23170198", "SRS20119595", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "non syn 5", "GSM8012739", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS|geo loc name:missing|collection date:missing", "non syn 5", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:non synchronized in response to CAS", "GSM8012739", "GSM8012739: non syn 5; Danio rerio; RNA Seq", "GSM8012739 r1", "GSM8012739", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "non-syn-5_S15_L003_R1_001.fastq.gz non-syn-5_S15_L003_R2_001.fastq.gz", "fastq fastq", 6694374900.0, 22314583.0, "GSM8012739 r1", "0:150 1:150", "A:1874497306;C:1098473614;G:1392771685;T:2328388616;N:243679", 150, 150, null, null, 1874497306, 1098473614, 1392771685, 2328388616, 243679, "SRX23170198", "SRS20119595", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29830, "SRR27499212", "SRX23170197", "SRS20119594", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 22", "GSM8012738", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 22", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012738", "GSM8012738: syn 22; Danio rerio; RNA Seq", "GSM8012738 r1", "GSM8012738", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-22_S1_L001_R1_001.fastq.gz syn-22_S1_L001_R2_001.fastq.gz", "fastq fastq", 2576962500.0, 8589875.0, "GSM8012738 r1", "0:150 1:150", "A:743952075;C:396567355;G:527169920;T:909228265;N:44885", 150, 150, null, null, 743952075, 396567355, 527169920, 909228265, 44885, "SRX23170197", "SRS20119594", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29831, "SRR27499213", "SRX23170196", "SRS20119593", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 21", "GSM8012737", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 21", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012737", "GSM8012737: syn 21; Danio rerio; RNA Seq", "GSM8012737 r1", "GSM8012737", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-21_S1_L001_R1_001.fastq.gz syn-21_S1_L001_R2_001.fastq.gz", "fastq fastq", 3139200000.0, 10464000.0, "GSM8012737 r1", "0:150 1:150", "A:906029209;C:480116580;G:641470237;T:1111517808;N:66166", 150, 150, null, null, 906029209, 480116580, 641470237, 1111517808, 66166, "SRX23170196", "SRS20119593", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29832, "SRR27499214", "SRX23170195", "SRS20119592", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 20", "GSM8012736", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 20", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012736", "GSM8012736: syn 20; Danio rerio; RNA Seq", "GSM8012736 r1", "GSM8012736", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-20_S17_L002_R1_001.fastq.gz syn-20_S17_L002_R2_001.fastq.gz", "fastq fastq", 4601500500.0, 15338335.0, "GSM8012736 r1", "0:150 1:150", "A:1288150411;C:745135993;G:1003148625;T:1564941023;N:124448", 150, 150, null, null, 1288150411, 745135993, 1003148625, 1564941023, 124448, "SRX23170195", "SRS20119592", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29833, "SRR27499215", "SRX23170194", "SRS20119591", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 16", "GSM8012735", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 16", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012735", "GSM8012735: syn 16; Danio rerio; RNA Seq", "GSM8012735 r1", "GSM8012735", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-16_S1_L001_R1_001.fastq.gz syn-16_S1_L001_R2_001.fastq.gz", "fastq fastq", 2566776900.0, 8555923.0, "GSM8012735 r1", "0:150 1:150", "A:714860453;C:407690072;G:525572866;T:918632205;N:21304", 150, 150, null, null, 714860453, 407690072, 525572866, 918632205, 21304, "SRX23170194", "SRS20119591", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29834, "SRR27499216", "SRX23170193", "SRS20119590", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 14 1", "GSM8012734", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 14 1", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012734", "GSM8012734: syn 14 1; Danio rerio; RNA Seq", "GSM8012734 r1", "GSM8012734", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-14-1_extract_R1.fastq syn-14-1_extract_R2.fastq", "fastq fastq", 3841698000.0, 12805660.0, "GSM8012734 r1", "0:150 1:150", "A:1155899190;C:576621004;G:728773344;T:1380391692;N:12770", 150, 150, null, null, 1155899190, 576621004, 728773344, 1380391692, 12770, "SRX23170193", "SRS20119590", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29835, "SRR27499217", "SRX23170192", "SRS20119589", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 9", "GSM8012733", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 9", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012733", "GSM8012733: syn 9; Danio rerio; RNA Seq", "GSM8012733 r1", "GSM8012733", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-9_S10_L002_R1_001.fastq.gz syn-9_S10_L002_R2_001.fastq.gz", "fastq fastq", 5141497200.0, 17138324.0, "GSM8012733 r1", "0:150 1:150", "A:1501566241;C:777725902;G:1012263041;T:1849766543;N:175473", 150, 150, null, null, 1501566241, 777725902, 1012263041, 1849766543, 175473, "SRX23170192", "SRS20119589", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29836, "SRR27499218", "SRX23170191", "SRS20119588", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 6", "GSM8012732", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 6", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012732", "GSM8012732: syn 6; Danio rerio; RNA Seq", "GSM8012732 r1", "GSM8012732", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-6_S5_L003_R1_001.fastq.gz syn-6_S5_L003_R2_001.fastq.gz", "fastq fastq", 3642350700.0, 12141169.0, "GSM8012732 r1", "0:150 1:150", "A:1017036453;C:585222109;G:725483108;T:1314599102;N:9928", 150, 150, null, null, 1017036453, 585222109, 725483108, 1314599102, 9928, "SRX23170191", "SRS20119588", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29837, "SRR27499219", "SRX23170190", "SRS20119587", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 5", "GSM8012731", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 5", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012731", "GSM8012731: syn 5; Danio rerio; RNA Seq", "GSM8012731 r1", "GSM8012731", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-5_S1_L001_R1_001.fastq.gz syn-5_S1_L001_R2_001.fastq.gz", "fastq fastq", 3446864400.0, 11489548.0, "GSM8012731 r1", "0:150 1:150", "A:1001098139;C:530696334;G:690506502;T:1224479197;N:84228", 150, 150, null, null, 1001098139, 530696334, 690506502, 1224479197, 84228, "SRX23170190", "SRS20119587", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29838, "SRR27499220", "SRX23170189", "SRS20119586", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 4 1", "GSM8012730", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 4 1", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012730", "GSM8012730: syn 4 1; Danio rerio; RNA Seq", "GSM8012730 r1", "GSM8012730", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-4-1_S5_L002_R1_001.fastq.gz syn-4-1_S5_L002_R2_001.fastq.gz", "fastq fastq", 5462793000.0, 18209310.0, "GSM8012730 r1", "0:150 1:150", "A:1468672385;C:876455469;G:1192232488;T:1925328687;N:103971", 150, 150, null, null, 1468672385, 876455469, 1192232488, 1925328687, 103971, "SRX23170189", "SRS20119586", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29839, "SRR27499221", "SRX23170188", "SRS20119585", "SRP483288", "PRJNA1063685", "Patch Seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment", "GSE253039", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment.TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette. Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions. RNA Seq libraries were sequenced using Illumina NextSeq 500  generating 75 bp paired end reads for each sample. RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. We identified differentially expressed genes DEGs between synchronized and non synchronized neurons in zebrafish dorsal pallium in response to CAS treatment. Synchronized neurons expressed much higher level of glutamate transporter genes slc17a7a  slc17a6a  while non synchronized neurons showed significantly higher expression of gad1b  suggesting that synchronized neurons are primarily glutamatergic  while non synchronized neurons are mainly GABAergic. Overall design: To distinguish neurons with synchronized or non synchronized calcium activity post CAS treatment  TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid and subjected to two photon imaging  and neurons were collected separately with glass pipette. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "pubmed:38519480", null, "syn 4", "GSM8012729", null, "source name:brain|tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS|geo loc name:missing|collection date:missing", "syn 4", "RNA Seq reads untrimmed. Differential expression analysis was performed using the CPM counts per million function in the Bioconductor package edgeR v 3.14.0. Low expression genes were excluded to make a simple correction for gene counts. Genes with P value instead of adjusted P value < 0.05 were assigned as differentially expressed. Assembly: danRer11 Supplementary files format and content: Excel file include readcounts values for each Sample.", "brain", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were fixed in a recording chamber containing extracellular fluid  and neurons with synchronized or non synchronized calcium activity post CAS treatment were identified by two photon imaging and collected separately with glass pipette.", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", "TgHuC:H2B GCaMP6f fish of 4 wpf 5 wpf were used.", "tissue:brain|strain:TgHuC:H2B GCaMP6f|cell type:neurons in dorsal pallium|treatment:synchronized in response to CAS", "GSM8012729", "GSM8012729: syn 4; Danio rerio; RNA Seq", "GSM8012729 r1", "GSM8012729", "1", "Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol Invitrogen and then purified on RNeasy columns Qiagen. Total RNA quality was assessed on a bioanalyzer Thermofisher. RNA Seq libraries N=10 for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP483288", null, null, "syn-4_S1_L001_R1_001.fastq.gz syn-4_S1_L001_R2_001.fastq.gz", "fastq fastq", 1890927900.0, 6303093.0, "GSM8012729 r1", "0:150 1:150", "A:516279078;C:299222574;G:422785519;T:652613922;N:26807", 150, 150, null, null, 516279078, 299222574, 422785519, 652613922, 26807, "SRX23170188", "SRS20119585", "SRA1784161", "Neuroscience, School of Medcine, Tongji University, 42508444-9", "Neuroscience, School of Medcine, Tongji University, 42508444-9", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2024-01-11", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30256, "SRR27747506", "SRX23412819", "SRS20268140", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Late born vestibular neurons  replicate 2", "GSM8038041", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede|geo loc name:missing|collection date:missing", "Late born vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede", "GSM8038041", "GSM8038041: Late born vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038041 r1", "GSM8038041", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Green_S19_L001_I1_001.fastq.gz Green_S19_L001_I2_001.fastq.gz Green_S19_L001_R1_001.fastq.gz Green_S19_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 4923159660.0, 35675070.0, "GSM8038041 r1", "0:10 1:10 2:28 3:90", "A:1637293866;C:391317121;G:716609880;T:465465343;N:70090", 10, 10, 28, 90, 1637293866, 391317121, 716609880, 465465343, 70090, "SRX23412819", "SRS20268140", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30257, "SRR27747507", "SRX23412819", "SRS20268140", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Late born vestibular neurons  replicate 2", "GSM8038041", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede|geo loc name:missing|collection date:missing", "Late born vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede", "GSM8038041", "GSM8038041: Late born vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038041 r1", "GSM8038041", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Green_S19_L002_I1_001.fastq.gz Green_S19_L002_I2_001.fastq.gz Green_S19_L002_R1_001.fastq.gz Green_S19_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 4858633206.0, 35207487.0, "GSM8038041 r2", "0:10 1:10 2:28 3:90", "A:1614338875;C:386568724;G:706765488;T:460927318;N:73425", 10, 10, 28, 90, 1614338875, 386568724, 706765488, 460927318, 73425, "SRX23412819", "SRS20268140", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30258, "SRR27747508", "SRX23412819", "SRS20268140", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Late born vestibular neurons  replicate 2", "GSM8038041", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede|geo loc name:missing|collection date:missing", "Late born vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede", "GSM8038041", "GSM8038041: Late born vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038041 r1", "GSM8038041", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Green_S19_L003_I1_001.fastq.gz Green_S19_L003_I2_001.fastq.gz Green_S19_L003_R1_001.fastq.gz Green_S19_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 4458723696.0, 32309592.0, "GSM8038041 r3", "0:10 1:10 2:28 3:90", "A:1463412697;C:359363166;G:655814899;T:429192204;N:80314", 10, 10, 28, 90, 1463412697, 359363166, 655814899, 429192204, 80314, "SRX23412819", "SRS20268140", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30259, "SRR27747509", "SRX23412819", "SRS20268140", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Late born vestibular neurons  replicate 2", "GSM8038041", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede|geo loc name:missing|collection date:missing", "Late born vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born post 36 hpf green unconverted Kaede", "GSM8038041", "GSM8038041: Late born vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038041 r1", "GSM8038041", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Green_S19_L004_I1_001.fastq.gz Green_S19_L004_I2_001.fastq.gz Green_S19_L004_R1_001.fastq.gz Green_S19_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 4425208602.0, 32066729.0, "GSM8038041 r4", "0:10 1:10 2:28 3:90", "A:1452148554;C:355763806;G:651302168;T:426718847;N:72235", 10, 10, 28, 90, 1452148554, 355763806, 651302168, 426718847, 72235, "SRX23412819", "SRS20268140", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30260, "SRR27747510", "SRX23412818", "SRS20268139", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Early born vestibular neurons  replicate 1", "GSM8038040", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede|geo loc name:missing|collection date:missing", "Early born vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede", "GSM8038040", "GSM8038040: Early born vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038040 r1", "GSM8038040", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Red_S20_L001_I1_001.fastq.gz Red_S20_L001_I2_001.fastq.gz Red_S20_L001_R1_001.fastq.gz Red_S20_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 5032560816.0, 36467832.0, "GSM8038040 r1", "0:10 1:10 2:28 3:90", "A:1626033872;C:414606578;G:755475703;T:485911557;N:77170", 10, 10, 28, 90, 1626033872, 414606578, 755475703, 485911557, 77170, "SRX23412818", "SRS20268139", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30261, "SRR27747511", "SRX23412818", "SRS20268139", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Early born vestibular neurons  replicate 1", "GSM8038040", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede|geo loc name:missing|collection date:missing", "Early born vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede", "GSM8038040", "GSM8038040: Early born vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038040 r1", "GSM8038040", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Red_S20_L002_I1_001.fastq.gz Red_S20_L002_I2_001.fastq.gz Red_S20_L002_R1_001.fastq.gz Red_S20_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 4998616680.0, 36221860.0, "GSM8038040 r2", "0:10 1:10 2:28 3:90", "A:1613203224;C:412246760;G:750087642;T:484348061;N:81713", 10, 10, 28, 90, 1613203224, 412246760, 750087642, 484348061, 81713, "SRX23412818", "SRS20268139", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30262, "SRR27747512", "SRX23412818", "SRS20268139", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Early born vestibular neurons  replicate 1", "GSM8038040", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede|geo loc name:missing|collection date:missing", "Early born vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede", "GSM8038040", "GSM8038040: Early born vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038040 r1", "GSM8038040", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Red_S20_L003_I1_001.fastq.gz Red_S20_L003_I2_001.fastq.gz Red_S20_L003_R1_001.fastq.gz Red_S20_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 4628879490.0, 33542605.0, "GSM8038040 r3", "0:10 1:10 2:28 3:90", "A:1475662550;C:386397974;G:701772418;T:454914612;N:86896", 10, 10, 28, 90, 1475662550, 386397974, 701772418, 454914612, 86896, "SRX23412818", "SRS20268139", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30263, "SRR27747513", "SRX23412818", "SRS20268139", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "Early born vestibular neurons  replicate 1", "GSM8038040", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede|geo loc name:missing|collection date:missing", "Early born vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:Neurons born before 36 hpf red photoconverted Kaede", "GSM8038040", "GSM8038040: Early born vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038040 r1", "GSM8038040", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Red_S20_L004_I1_001.fastq.gz Red_S20_L004_I2_001.fastq.gz Red_S20_L004_R1_001.fastq.gz Red_S20_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 4582808190.0, 33208755.0, "GSM8038040 r4", "0:10 1:10 2:28 3:90", "A:1460627048;C:381772307;G:695044521;T:451264941;N:79133", 10, 10, 28, 90, 1460627048, 381772307, 695044521, 451264941, 79133, "SRX23412818", "SRS20268139", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30264, "SRR27747514", "SRX23412817", "SRS20268138", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 3", "GSM8038039", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 3", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038039", "GSM8038039: All vestibular neurons  replicate 3; Danio rerio; RNA Seq", "GSM8038039 r1", "GSM8038039", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate3_S3_L001_I1_001.fastq.gz Zebrafish-Replicate3_S3_L001_I2_001.fastq.gz Zebrafish-Replicate3_S3_L001_R1_001.fastq.gz Zebrafish-Replicate3_S3_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 10560652880.0, 75975920.0, "GSM8038039 r1", "0:10 1:10 2:28 3:91", "A:2623816838;C:1175510072;G:1638990770;T:1474946754;N:544286", 10, 10, 28, 91, 2623816838, 1175510072, 1638990770, 1474946754, 544286, "SRX23412817", "SRS20268138", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30265, "SRR27747515", "SRX23412817", "SRS20268138", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 3", "GSM8038039", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 3", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038039", "GSM8038039: All vestibular neurons  replicate 3; Danio rerio; RNA Seq", "GSM8038039 r1", "GSM8038039", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate3_S3_L002_I1_001.fastq.gz Zebrafish-Replicate3_S3_L002_I2_001.fastq.gz Zebrafish-Replicate3_S3_L002_R1_001.fastq.gz Zebrafish-Replicate3_S3_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 10571317933.0, 76052647.0, "GSM8038039 r2", "0:10 1:10 2:28 3:91", "A:2631345994;C:1175630391;G:1641110007;T:1472183634;N:520851", 10, 10, 28, 91, 2631345994, 1175630391, 1641110007, 1472183634, 520851, "SRX23412817", "SRS20268138", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30266, "SRR27747516", "SRX23412817", "SRS20268138", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 3", "GSM8038039", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 3", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038039", "GSM8038039: All vestibular neurons  replicate 3; Danio rerio; RNA Seq", "GSM8038039 r1", "GSM8038039", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate3_S3_L003_I1_001.fastq.gz Zebrafish-Replicate3_S3_L003_I2_001.fastq.gz Zebrafish-Replicate3_S3_L003_R1_001.fastq.gz Zebrafish-Replicate3_S3_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 10457106081.0, 75230979.0, "GSM8038039 r3", "0:10 1:10 2:28 3:91", "A:2588687752;C:1168371662;G:1623033341;T:1465362298;N:564036", 10, 10, 28, 91, 2588687752, 1168371662, 1623033341, 1465362298, 564036, "SRX23412817", "SRS20268138", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30267, "SRR27747517", "SRX23412817", "SRS20268138", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 3", "GSM8038039", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 3", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038039", "GSM8038039: All vestibular neurons  replicate 3; Danio rerio; RNA Seq", "GSM8038039 r1", "GSM8038039", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate3_S3_L004_I1_001.fastq.gz Zebrafish-Replicate3_S3_L004_I2_001.fastq.gz Zebrafish-Replicate3_S3_L004_R1_001.fastq.gz Zebrafish-Replicate3_S3_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 10455949462.0, 75222658.0, "GSM8038039 r4", "0:10 1:10 2:28 3:91", "A:2581792541;C:1170458560;G:1624194611;T:1468248274;N:567892", 10, 10, 28, 91, 2581792541, 1170458560, 1624194611, 1468248274, 567892, "SRX23412817", "SRS20268138", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30268, "SRR27747518", "SRX23412816", "SRS20268137", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 2", "GSM8038038", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038038", "GSM8038038: All vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038038 r1", "GSM8038038", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate2_S2_L001_I1_001.fastq.gz Zebrafish-Replicate2_S2_L001_I2_001.fastq.gz Zebrafish-Replicate2_S2_L001_R1_001.fastq.gz Zebrafish-Replicate2_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 9414131535.0, 67727565.0, "GSM8038038 r1", "0:10 1:10 2:28 3:91", "A:2659651693;C:894536960;G:1598721159;T:1009819179;N:479424", 10, 10, 28, 91, 2659651693, 894536960, 1598721159, 1009819179, 479424, "SRX23412816", "SRS20268137", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30269, "SRR27747519", "SRX23412816", "SRS20268137", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 2", "GSM8038038", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038038", "GSM8038038: All vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038038 r1", "GSM8038038", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate2_S2_L002_I1_001.fastq.gz Zebrafish-Replicate2_S2_L002_I2_001.fastq.gz Zebrafish-Replicate2_S2_L002_R1_001.fastq.gz Zebrafish-Replicate2_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 9495760675.0, 68314825.0, "GSM8038038 r2", "0:10 1:10 2:28 3:91", "A:2685940540;C:901627244;G:1612080998;T:1016532106;N:468187", 10, 10, 28, 91, 2685940540, 901627244, 1612080998, 1016532106, 468187, "SRX23412816", "SRS20268137", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30270, "SRR27747520", "SRX23412816", "SRS20268137", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 2", "GSM8038038", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038038", "GSM8038038: All vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038038 r1", "GSM8038038", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate2_S2_L003_I1_001.fastq.gz Zebrafish-Replicate2_S2_L003_I2_001.fastq.gz Zebrafish-Replicate2_S2_L003_R1_001.fastq.gz Zebrafish-Replicate2_S2_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 9299053574.0, 66899666.0, "GSM8038038 r3", "0:10 1:10 2:28 3:91", "A:2619668178;C:887003175;G:1580306677;T:1000391033;N:500543", 10, 10, 28, 91, 2619668178, 887003175, 1580306677, 1000391033, 500543, "SRX23412816", "SRS20268137", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30271, "SRR27747521", "SRX23412816", "SRS20268137", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 2", "GSM8038038", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 2", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038038", "GSM8038038: All vestibular neurons  replicate 2; Danio rerio; RNA Seq", "GSM8038038 r1", "GSM8038038", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate2_S2_L004_I1_001.fastq.gz Zebrafish-Replicate2_S2_L004_I2_001.fastq.gz Zebrafish-Replicate2_S2_L004_R1_001.fastq.gz Zebrafish-Replicate2_S2_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 9269439763.0, 66686617.0, "GSM8038038 r4", "0:10 1:10 2:28 3:91", "A:2605497678;C:885933483;G:1577360287;T:999190994;N:499705", 10, 10, 28, 91, 2605497678, 885933483, 1577360287, 999190994, 499705, "SRX23412816", "SRS20268137", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30272, "SRR27747522", "SRX23412815", "SRS20268136", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 1", "GSM8038037", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038037", "GSM8038037: All vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038037 r1", "GSM8038037", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate1_S1_L001_I1_001.fastq.gz Zebrafish-Replicate1_S1_L001_I2_001.fastq.gz Zebrafish-Replicate1_S1_L001_R1_001.fastq.gz Zebrafish-Replicate1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 11844241708.0, 85210372.0, "GSM8038037 r1", "0:10 1:10 2:28 3:91", "A:3114181870;C:1253864519;G:2080987238;T:1304504811;N:605414", 10, 10, 28, 91, 3114181870, 1253864519, 2080987238, 1304504811, 605414, "SRX23412815", "SRS20268136", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30273, "SRR27747523", "SRX23412815", "SRS20268136", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 1", "GSM8038037", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038037", "GSM8038037: All vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038037 r1", "GSM8038037", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate1_S1_L002_I1_001.fastq.gz Zebrafish-Replicate1_S1_L002_I2_001.fastq.gz Zebrafish-Replicate1_S1_L002_R1_001.fastq.gz Zebrafish-Replicate1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11897506230.0, 85593570.0, "GSM8038037 r2", "0:10 1:10 2:28 3:91", "A:3132719148;C:1257962906;G:2089627351;T:1308117927;N:587538", 10, 10, 28, 91, 3132719148, 1257962906, 2089627351, 1308117927, 587538, "SRX23412815", "SRS20268136", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30274, "SRR27747524", "SRX23412815", "SRS20268136", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 1", "GSM8038037", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038037", "GSM8038037: All vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038037 r1", "GSM8038037", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate1_S1_L003_I1_001.fastq.gz Zebrafish-Replicate1_S1_L003_I2_001.fastq.gz Zebrafish-Replicate1_S1_L003_R1_001.fastq.gz Zebrafish-Replicate1_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 11710536913.0, 84248467.0, "GSM8038037 r3", "0:10 1:10 2:28 3:91", "A:3071431897;C:1243257065;G:2058561915;T:1292732765;N:626855", 10, 10, 28, 91, 3071431897, 1243257065, 2058561915, 1292732765, 626855, "SRX23412815", "SRS20268136", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30275, "SRR27747525", "SRX23412815", "SRS20268136", "SRP486180", "PRJNA1069776", "Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq", "GSE254346", "Transcriptome Analysis", "The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate  topography  and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons  labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede  harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified \"midpoint\" in hindbrain vestibular neuron development 36 hpf  labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.", null, null, null, "All vestibular neurons  replicate 1", "GSM8038037", null, "tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing", "All vestibular neurons  replicate 1", "Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Hindbrain vestibular neurons", "Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red  converted Kaede from late born green  unconverted Kaede neurons.", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a", "GSM8038037", "GSM8038037: All vestibular neurons  replicate 1; Danio rerio; RNA Seq", "GSM8038037 r1", "GSM8038037", "1", "Harvested neurons were sorted to isolate single cells  resuspended in L15+2% FBS  and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics  three prime V3.1", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP486180", null, "loader:fastq load.py", "Zebrafish-Replicate1_S1_L004_I1_001.fastq.gz Zebrafish-Replicate1_S1_L004_I2_001.fastq.gz Zebrafish-Replicate1_S1_L004_R1_001.fastq.gz Zebrafish-Replicate1_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 11691727294.0, 84113146.0, "GSM8038037 r4", "0:10 1:10 2:28 3:91", "A:3060624267;C:1243160034;G:2057238308;T:1292649886;N:623791", 10, 10, 28, 91, 3060624267, 1243160034, 2057238308, 1292649886, 623791, "SRX23412815", "SRS20268136", "SRA1792542", "Neuroscience Institute, New York University Grossman School of Medicine", "Neuroscience Institute, New York University Grossman School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-01-26", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [30691, "SRR28270998", "SRX23880961", "SRS20704477", "SRP494117", "PRJNA1085662", "Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells", "PRJNA1085662", "Other", "Roxithromycin ROX  a commonly used macrolide antibiotic  is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation  ROX persists as a resilient environmental contaminant  detectable in aquatic ecosystems and food products. However  our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study  we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure  particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos  significantly reducing hatch rates  body lengths  and increased malformation rates. Moreover  ROX exposure adversely affected the locomotive capacity of zebrafish embryos  and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons  evident through reduced or irregular axonal lengths. Concurrently  abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax  bcl2  caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1  olig2  axon development cd82a  mbpa  plp1b  sema5a  and neuroimmunity aplnrb  aplnra in zebrafish larvae. Furthermore  the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary  ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.", null, null, null, null, "WT", null, "strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells", "DANIO", "DANIO", "Illumina Second Generation Sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_oligo_dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP494117", null, null, "WT_S1_L001_I1_001.fastq.gz", "fastq", 7991376264.0, 998922033.0, "WT S1 L001 I1 001.fastq.gz", "0:8", "A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175", 8, null, null, null, 2573734851, 1426474966, 1492966198, 2498173074, 27175, "SRX23880961", "SRS20704477", "SRA1820072", "shantou university|Neurobiology Center", "shantou university", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-03-11", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33194, "SRR29848455", "SRX25346236", "SRS22013450", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf brain replicate4", "GSM8399288", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf brain replicate4", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf", "GSM8399288", "GSM8399288: IPP 120hpf brain replicate4; Danio rerio; RNA Seq", "GSM8399288 r1", "GSM8399288", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "IPP_br_4_2.fq.gz IPP_br_4_1.fq.gz", "fastq fastq", 9390779700.0, 31302599.0, "GSM8399288 r1", "0:150 1:150", "A:2560313119;C:2151676461;G:2133189890;T:2537450452;N:8149778", 150, 150, null, null, 2560313119, 2151676461, 2133189890, 2537450452, 8149778, "SRX25346236", "SRS22013450", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.91404, 0.90534, 0.11908, 0.11758, 0.6857, 0.68586, 0.48538, 0.48727, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33195, "SRR29848456", "SRX25346235", "SRS22013449", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf brain replicate3", "GSM8399287", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf brain replicate3", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf", "GSM8399287", "GSM8399287: IPP 120hpf brain replicate3; Danio rerio; RNA Seq", "GSM8399287 r1", "GSM8399287", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "IPP_br_3_2.fq.gz IPP_br_3_1.fq.gz", "fastq fastq", 9990783900.0, 33302613.0, "GSM8399287 r1", "0:150 1:150", "A:2754200649;C:2263241737;G:2240476414;T:2724074441;N:8790659", 150, 150, null, null, 2754200649, 2263241737, 2240476414, 2724074441, 8790659, "SRX25346235", "SRS22013449", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.89342, 0.88652, 0.13588, 0.13469, 0.69619, 0.69873, 0.48918, 0.4915, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33196, "SRR29848457", "SRX25346234", "SRS22013448", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf brain replicate2", "GSM8399286", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf brain replicate2", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf", "GSM8399286", "GSM8399286: IPP 120hpf brain replicate2; Danio rerio; RNA Seq", "GSM8399286 r1", "GSM8399286", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "IPP_br_2_2.fq.gz IPP_br_2_1.fq.gz", "fastq fastq", 7422581400.0, 24741938.0, "GSM8399286 r1", "0:150 1:150", "A:1991481567;C:1733585261;G:1717902490;T:1973083455;N:6528627", 150, 150, null, null, 1991481567, 1733585261, 1717902490, 1973083455, 6528627, "SRX25346234", "SRS22013448", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.71292, 0.7054, 0.1035, 0.10212, 0.72661, 0.72742, 0.47375, 0.47346, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33197, "SRR29848458", "SRX25346233", "SRS22013447", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf brain replicate1", "GSM8399285", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf brain replicate1", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:IPP|time:120hpf", "GSM8399285", "GSM8399285: IPP 120hpf brain replicate1; Danio rerio; RNA Seq", "GSM8399285 r1", "GSM8399285", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "IPP_br_1_2.fq.gz IPP_br_1_1.fq.gz", "fastq fastq", 7045697400.0, 23485658.0, "GSM8399285 r1", "0:150 1:150", "A:1917558366;C:1619481314;G:1604633678;T:1897790571;N:6233471", 150, 150, null, null, 1917558366, 1619481314, 1604633678, 1897790571, 6233471, "SRX25346233", "SRS22013447", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.85861, 0.85026, 0.1263, 0.12558, 0.71023, 0.71212, 0.48933, 0.48746, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33198, "SRR29848459", "SRX25346232", "SRS22013446", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf brain replicate4", "GSM8399284", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf brain replicate4", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399284", "GSM8399284: DMSO 120hpf brain replicate4; Danio rerio; RNA Seq", "GSM8399284 r1", "GSM8399284", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_br_4_1.fq.gz Ctrl_br_4_2.fq.gz", "fastq fastq", 7179947400.0, 23933158.0, "GSM8399284 r1", "0:150 1:150", "A:1966898007;C:1638394745;G:1623410295;T:1945048506;N:6195847", 150, 150, null, null, 1966898007, 1638394745, 1623410295, 1945048506, 6195847, "SRX25346232", "SRS22013446", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.89488, 0.88555, 0.13181, 0.13042, 0.69341, 0.69422, 0.48804, 0.48947, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33199, "SRR29848460", "SRX25346231", "SRS22013445", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf brain replicate3", "GSM8399283", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf brain replicate3", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399283", "GSM8399283: DMSO 120hpf brain replicate3; Danio rerio; RNA Seq", "GSM8399283 r1", "GSM8399283", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_br_3_1.fq.gz Ctrl_br_3_2.fq.gz", "fastq fastq", 7565549100.0, 25218497.0, "GSM8399283 r1", "0:150 1:150", "A:2083415263;C:1715858147;G:1698292009;T:2061406404;N:6577277", 150, 150, null, null, 2083415263, 1715858147, 1698292009, 2061406404, 6577277, "SRX25346231", "SRS22013445", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.90542, 0.89696, 0.13734, 0.1367, 0.70356, 0.70483, 0.48312, 0.48368, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33200, "SRR29848461", "SRX25346230", "SRS22013444", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf brain replicate2", "GSM8399282", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf brain replicate2", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399282", "GSM8399282: DMSO 120hpf brain replicate2; Danio rerio; RNA Seq", "GSM8399282 r1", "GSM8399282", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_br_2_1.fq.gz Ctrl_br_2_2.fq.gz", "fastq fastq", 6365523600.0, 21218412.0, "GSM8399282 r1", "0:150 1:150", "A:1750052740;C:1446847379;G:1433401005;T:1729867036;N:5355440", 150, 150, null, null, 1750052740, 1446847379, 1433401005, 1729867036, 5355440, "SRX25346230", "SRS22013444", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.87816, 0.86877, 0.13095, 0.12991, 0.71417, 0.71545, 0.48949, 0.48793, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33201, "SRR29848462", "SRX25346229", "SRS22013443", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "DMSO 120hpf brain replicate1", "GSM8399281", null, "source name:Dissected brain|tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing", "DMSO 120hpf brain replicate1", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected brain", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected brain|genotype:wildtype|treatment:DMSO|time:120hpf", "GSM8399281", "GSM8399281: DMSO 120hpf brain replicate1; Danio rerio; RNA Seq", "GSM8399281 r1", "GSM8399281", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "Ctrl_br_1_1.fq.gz Ctrl_br_1_2.fq.gz", "fastq fastq", 6824090400.0, 22746968.0, "GSM8399281 r1", "0:150 1:150", "A:1885413177;C:1542704161;G:1526663517;T:1868806756;N:502789", 150, 150, null, null, 1885413177, 1542704161, 1526663517, 1868806756, 502789, "SRX25346229", "SRS22013443", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.91195, 0.90386, 0.13707, 0.13478, 0.70469, 0.7065, 0.48937, 0.49265, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [33254, "SRR29884387", "SRX25380731", "SRS22046084", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Male 5", "GSM8406341", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406341", "GSM8406341: Eye  wh5  Male 5; Danio rerio; RNA Seq", "GSM8406341 r1", "GSM8406341", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample40KOMaleEye_R2.fastq Sample40KOMaleEye_R1.fastq", "fastq fastq", 7538485922.0, 39271929.0, "GSM8406341 r1", "0:95.98 1:95.98", "A:1967237212;C:1781996027;G:1815934363;T:1970640817;N:2677503", 95, 95, null, null, 1967237212, 1781996027, 1815934363, 1970640817, 2677503, "SRX25380731", "SRS22046084", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.95183, 0.95218, 0.07853, 0.07764, 0.68146, 0.68166, 0.49087, 0.49177, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33255, "SRR29884388", "SRX25380730", "SRS22046083", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Male 4", "GSM8406340", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406340", "GSM8406340: Eye  wh5  Male 4; Danio rerio; RNA Seq", "GSM8406340 r1", "GSM8406340", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample39KOMaleEye_R1.fastq Sample39KOMaleEye_R2.fastq", "fastq fastq", 7862494596.0, 40297814.0, "GSM8406340 r1", "0:97.55 1:97.55", "A:2107320803;C:1803034371;G:1842789416;T:2106566245;N:2783761", 97, 97, null, null, 2107320803, 1803034371, 1842789416, 2106566245, 2783761, "SRX25380730", "SRS22046083", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.88885, 0.89107, 0.07613, 0.07476, 0.69451, 0.69566, 0.49352, 0.50029, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33256, "SRR29884389", "SRX25380729", "SRS22046082", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Male 3", "GSM8406339", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406339", "GSM8406339: Eye  wh5  Male 3; Danio rerio; RNA Seq", "GSM8406339 r1", "GSM8406339", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample38KOMaleEye_R1.fastq Sample38KOMaleEye_R2.fastq", "fastq fastq", 6479297470.0, 32901327.0, "GSM8406339 r1", "0:98.47 1:98.47", "A:1738119915;C:1487098061;G:1513025225;T:1738788853;N:2265416", 98, 98, null, null, 1738119915, 1487098061, 1513025225, 1738788853, 2265416, "SRX25380729", "SRS22046082", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94562, 0.94732, 0.07992, 0.07909, 0.69158, 0.69138, 0.50829, 0.5024, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33257, "SRR29884390", "SRX25380728", "SRS22046081", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Male 2", "GSM8406338", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406338", "GSM8406338: Eye  wh5  Male 2; Danio rerio; RNA Seq", "GSM8406338 r1", "GSM8406338", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample37KOMaleEye_R1.fastq Sample37KOMaleEye_R2.fastq", "fastq fastq", 6629719076.0, 33727364.0, "GSM8406338 r1", "0:98.28 1:98.28", "A:1764705315;C:1534928212;G:1563035445;T:1764737150;N:2312954", 98, 98, null, null, 1764705315, 1534928212, 1563035445, 1764737150, 2312954, "SRX25380728", "SRS22046081", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.95253, 0.95618, 0.07586, 0.07516, 0.69282, 0.69221, 0.49593, 0.4823, 69, 69, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33258, "SRR29884391", "SRX25380727", "SRS22046080", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Male 1", "GSM8406337", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406337", "GSM8406337: Eye  wh5  Male 1; Danio rerio; RNA Seq", "GSM8406337 r1", "GSM8406337", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample36KOMaleEye_R1.fastq Sample36KOMaleEye_R2.fastq", "fastq fastq", 5709061918.0, 28979886.0, "GSM8406337 r1", "0:98.50 1:98.50", "A:1522981393;C:1321621825;G:1340646747;T:1521818110;N:1993843", 98, 98, null, null, 1522981393, 1321621825, 1340646747, 1521818110, 1993843, "SRX25380727", "SRS22046080", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94615, 0.94747, 0.11492, 0.11272, 0.68436, 0.68446, 0.51813, 0.5179, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33259, "SRR29884392", "SRX25380726", "SRS22046079", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Female 5", "GSM8406336", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406336", "GSM8406336: Eye  wh5  Female 5; Danio rerio; RNA Seq", "GSM8406336 r1", "GSM8406336", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample35KOFemaleEye_R1.fastq Sample35KOFemaleEye_R2.fastq", "fastq fastq", 5427070458.0, 28381536.0, "GSM8406336 r1", "0:95.61 1:95.61", "A:1415064176;C:1287586920;G:1304802479;T:1417689072;N:1927811", 95, 95, null, null, 1415064176, 1287586920, 1304802479, 1417689072, 1927811, "SRX25380726", "SRS22046079", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94227, 0.94361, 0.11567, 0.11449, 0.67452, 0.67442, 0.49494, 0.49637, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33260, "SRR29884393", "SRX25380725", "SRS22046078", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Female 4", "GSM8406335", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406335", "GSM8406335: Eye  wh5  Female 4; Danio rerio; RNA Seq", "GSM8406335 r1", "GSM8406335", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample34KOFemaleEye_R1.fastq Sample34KOFemaleEye_R2.fastq", "fastq fastq", 7147923902.0, 36321130.0, "GSM8406335 r1", "0:98.40 1:98.40", "A:1915214130;C:1645720125;G:1671289633;T:1913205077;N:2494937", 98, 98, null, null, 1915214130, 1645720125, 1671289633, 1913205077, 2494937, "SRX25380725", "SRS22046078", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94673, 0.9495, 0.10846, 0.10716, 0.68546, 0.68576, 0.50162, 0.51282, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33261, "SRR29884394", "SRX25380724", "SRS22046077", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Female 3", "GSM8406334", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406334", "GSM8406334: Eye  wh5  Female 3; Danio rerio; RNA Seq", "GSM8406334 r1", "GSM8406334", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample33KOFemaleEye_R1.fastq Sample33KOFemaleEye_R2.fastq", "fastq fastq", 5282619330.0, 26862421.0, "GSM8406334 r1", "0:98.33 1:98.33", "A:1401322632;C:1228726745;G:1250721810;T:1400000047;N:1848096", 98, 98, null, null, 1401322632, 1228726745, 1250721810, 1400000047, 1848096, "SRX25380724", "SRS22046077", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94918, 0.95136, 0.09986, 0.09846, 0.68406, 0.68343, 0.50791, 0.50912, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33262, "SRR29884395", "SRX25380723", "SRS22046076", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Female 2", "GSM8406333", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406333", "GSM8406333: Eye  wh5  Female 2; Danio rerio; RNA Seq", "GSM8406333 r1", "GSM8406333", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample32KOFemaleEye_R1.fastq Sample32KOFemaleEye_R2.fastq", "fastq fastq", 5138054606.0, 26117176.0, "GSM8406333 r1", "0:98.37 1:98.37", "A:1362190516;C:1195339408;G:1217795589;T:1360934102;N:1794991", 98, 98, null, null, 1362190516, 1195339408, 1217795589, 1360934102, 1794991, "SRX25380723", "SRS22046076", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.95053, 0.95112, 0.11959, 0.11702, 0.68564, 0.68487, 0.53365, 0.52549, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33263, "SRR29884396", "SRX25380722", "SRS22046075", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  wh5  Female 1", "GSM8406332", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye  wh5  Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406332", "GSM8406332: Eye  wh5  Female 1; Danio rerio; RNA Seq", "GSM8406332 r1", "GSM8406332", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample31KOFemaleEye_R1.fastq Sample31KOFemaleEye_R2.fastq", "fastq fastq", 10220677680.0, 51930769.0, "GSM8406332 r1", "0:98.41 1:98.41", "A:2678910180;C:2403108978;G:2460841265;T:2674251113;N:3566144", 98, 98, null, null, 2678910180, 2403108978, 2460841265, 2674251113, 3566144, "SRX25380722", "SRS22046075", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94832, 0.95149, 0.11677, 0.11536, 0.69199, 0.69144, 0.51108, 0.51355, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33264, "SRR29884397", "SRX25380721", "SRS22046073", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Male 5", "GSM8406331", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406331", "GSM8406331: Eye  WT  Male 5; Danio rerio; RNA Seq", "GSM8406331 r1", "GSM8406331", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample30WTMaleEye_R1.fastq Sample30WTMaleEye_R2.fastq", "fastq fastq", 6485687400.0, 33002416.0, "GSM8406331 r1", "0:98.26 1:98.26", "A:1728466253;C:1500931006;G:1524828714;T:1729195053;N:2266374", 98, 98, null, null, 1728466253, 1500931006, 1524828714, 1729195053, 2266374, "SRX25380721", "SRS22046073", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94722, 0.94937, 0.10433, 0.10291, 0.68883, 0.68939, 0.49445, 0.46638, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33265, "SRR29884398", "SRX25380720", "SRS22046074", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Male 4", "GSM8406330", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406330", "GSM8406330: Eye  WT  Male 4; Danio rerio; RNA Seq", "GSM8406330 r1", "GSM8406330", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample29WTMaleEye_R1.fastq Sample29WTMaleEye_R2.fastq", "fastq fastq", 7062083656.0, 35791158.0, "GSM8406330 r1", "0:98.66 1:98.66", "A:1894520544;C:1621849694;G:1646676208;T:1896586465;N:2450745", 98, 98, null, null, 1894520544, 1621849694, 1646676208, 1896586465, 2450745, "SRX25380720", "SRS22046074", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.9467, 0.94857, 0.11004, 0.1075, 0.68657, 0.686, 0.50982, 0.50696, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33266, "SRR29884399", "SRX25380719", "SRS22046072", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Male 3", "GSM8406329", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406329", "GSM8406329: Eye  WT  Male 3; Danio rerio; RNA Seq", "GSM8406329 r1", "GSM8406329", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample28WTMaleEye_R2.fastq Sample28WTMaleEye_R1.fastq", "fastq fastq", 6460573656.0, 32912157.0, "GSM8406329 r1", "0:98.15 1:98.15", "A:1734329877;C:1484525299;G:1504584680;T:1734881748;N:2252052", 98, 98, null, null, 1734329877, 1484525299, 1504584680, 1734881748, 2252052, "SRX25380719", "SRS22046072", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94094, 0.94266, 0.11467, 0.113, 0.68574, 0.68511, 0.52613, 0.49429, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33267, "SRR29884400", "SRX25380718", "SRS22046071", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Male 2", "GSM8406328", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406328", "GSM8406328: Eye  WT  Male 2; Danio rerio; RNA Seq", "GSM8406328 r1", "GSM8406328", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample27WTMaleEye_R1.fastq Sample27WTMaleEye_R2.fastq", "fastq fastq", 8379349662.0, 42809191.0, "GSM8406328 r1", "0:97.87 1:97.87", "A:2236044006;C:1937171487;G:1969824761;T:2233423000;N:2886408", 97, 97, null, null, 2236044006, 1937171487, 1969824761, 2233423000, 2886408, "SRX25380718", "SRS22046071", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94985, 0.95265, 0.0973, 0.09565, 0.68814, 0.68868, 0.49928, 0.50187, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33268, "SRR29884401", "SRX25380717", "SRS22046070", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Male 1", "GSM8406327", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406327", "GSM8406327: Eye  WT  Male 1; Danio rerio; RNA Seq", "GSM8406327 r1", "GSM8406327", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample26WTMaleEye_R1.fastq Sample26WTMaleEye_R2.fastq", "fastq fastq", 6903877724.0, 35162472.0, "GSM8406327 r1", "0:98.17 1:98.17", "A:1834111504;C:1600540211;G:1632902994;T:1833911892;N:2411123", 98, 98, null, null, 1834111504, 1600540211, 1632902994, 1833911892, 2411123, "SRX25380717", "SRS22046070", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94845, 0.94881, 0.10868, 0.106, 0.68684, 0.68647, 0.51253, 0.51184, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33269, "SRR29884402", "SRX25380716", "SRS22046069", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Female 5", "GSM8406326", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406326", "GSM8406326: Eye  WT  Female 5; Danio rerio; RNA Seq", "GSM8406326 r1", "GSM8406326", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample25WTFemaleEye_R1.fastq Sample25WTFemaleEye_R2.fastq", "fastq fastq", 6008109144.0, 30559574.0, "GSM8406326 r1", "0:98.30 1:98.30", "A:1602153382;C:1384849253;G:1417624141;T:1601373961;N:2108407", 98, 98, null, null, 1602153382, 1384849253, 1417624141, 1601373961, 2108407, "SRX25380716", "SRS22046069", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94455, 0.94527, 0.11551, 0.11357, 0.68294, 0.68337, 0.52076, 0.51087, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33270, "SRR29884403", "SRX25380715", "SRS22046068", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Female 4", "GSM8406325", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406325", "GSM8406325: Eye  WT  Female 4; Danio rerio; RNA Seq", "GSM8406325 r1", "GSM8406325", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample24WTFemaleEye_R1.fastq Sample24WTFemaleEye_R2.fastq", "fastq fastq", 7279680362.0, 36932422.0, "GSM8406325 r1", "0:98.55 1:98.55", "A:1970880191;C:1653556002;G:1681116124;T:1971590390;N:2537655", 98, 98, null, null, 1970880191, 1653556002, 1681116124, 1971590390, 2537655, "SRX25380715", "SRS22046068", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94446, 0.945, 0.11353, 0.11157, 0.69053, 0.69002, 0.51519, 0.51315, 90, 90, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33271, "SRR29884404", "SRX25380714", "SRS22046067", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye  WT  Female 3", "GSM8406324", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye  WT  Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406324", "GSM8406324: Eye  WT  Female 3; Danio rerio; RNA Seq", "GSM8406324 r1", "GSM8406324", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample23WTFemaleEye_R1.fastq Sample23WTFemaleEye_R2.fastq", "fastq fastq", 5569794970.0, 28366560.0, "GSM8406324 r1", "0:98.18 1:98.18", "A:1484725199;C:1288582787;G:1309580985;T:1484962225;N:1943774", 98, 98, null, null, 1484725199, 1288582787, 1309580985, 1484962225, 1943774, "SRX25380714", "SRS22046067", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94662, 0.94876, 0.11169, 0.10977, 0.68783, 0.68738, 0.49232, 0.49903, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 243, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", 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[experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, 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