{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"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"], [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"], [34088, "SRR31047783", "SRX26432306", "SRS22949546", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 3", "GSM8582553", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 3", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582553", "GSM8582553: 6PPD 3; Danio rerio; RNA Seq", "GSM8582553 r1", "GSM8582553", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD3head_Clean_Data1.fq.gz 6PPD3head_Clean_Data2.fq.gz", "fastq fastq", 5643201065.0, 19058349.0, "GSM8582553 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432306", "SRS22949546", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34089, "SRR31047784", "SRX26432305", "SRS22949545", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 2", "GSM8582552", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 2", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582552", "GSM8582552: 6PPD 2; Danio rerio; RNA Seq", "GSM8582552 r1", "GSM8582552", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD2head_Clean_Data1.fq.gz 6PPD2head_Clean_Data2.fq.gz", "fastq fastq", 6184525960.0, 20877930.0, "GSM8582552 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432305", "SRS22949545", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34090, "SRR31047785", "SRX26432304", "SRS22949544", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 1", "GSM8582551", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 1", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582551", "GSM8582551: 6PPD 1; Danio rerio; RNA Seq", "GSM8582551 r1", "GSM8582551", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD1head_Clean_Data1.fq.gz 6PPD1head_Clean_Data2.fq.gz", "fastq fastq", 5412472152.0, 18274114.0, "GSM8582551 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432304", "SRS22949544", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34091, "SRR31047786", "SRX26432303", "SRS22949543", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "Con 3", "GSM8582550", null, "source name:Brain|tissue:Brain|treatment:DMSO|geo loc name:missing|collection date:missing", "Con 3", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:DMSO", "GSM8582550", "GSM8582550: Con 3; Danio rerio; RNA Seq", "GSM8582550 r1", "GSM8582550", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "Con3head_Clean_Data1.fq.gz Con3head_Clean_Data2.fq.gz", "fastq fastq", 6118959402.0, 20641047.0, "GSM8582550 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432303", "SRS22949543", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34092, "SRR31047787", "SRX26432302", "SRS22949542", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "Con 2", "GSM8582549", null, "source name:Brain|tissue:Brain|treatment:DMSO|geo loc name:missing|collection date:missing", "Con 2", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:DMSO", "GSM8582549", "GSM8582549: Con 2; Danio rerio; RNA Seq", "GSM8582549 r1", "GSM8582549", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "Con2head_Clean_Data1.fq.gz Con2head_Clean_Data2.fq.gz", "fastq fastq", 5778620515.0, 19519984.0, "GSM8582549 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432302", "SRS22949542", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34093, "SRR31047788", "SRX26432301", "SRS22949541", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "Con 1", "GSM8582548", null, "source name:Brain|tissue:Brain|treatment:DMSO|geo loc name:missing|collection date:missing", "Con 1", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:DMSO", "GSM8582548", "GSM8582548: Con 1; Danio rerio; RNA Seq", "GSM8582548 r1", "GSM8582548", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "Con1head_Clean_Data1.fq.gz Con1head_Clean_Data2.fq.gz", "fastq fastq", 5538973366.0, 18707123.0, "GSM8582548 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432301", "SRS22949541", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [37259, "SRR1049956", "SRX392057", "SRS515268", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Treated biological replicate 3", "GSM1289435", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "Treated biological replicate 3", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "GSM1289435", "GSM1289435: Treated biological replicate 3; Danio rerio; RNA Seq", "GSM1289435", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_13_index23_GAGTGG_L008_R2.fastq.gz TFJN03_13_index23_GAGTGG_L008_R1.fastq.gz", "fastq fastq", 5190526000.0, 25952630.0, "GSM1289435 r1", "0:100 1:100", "A:1460493081;C:1094348356;G:1181016291;T:1437219675;N:17448597", 100, 100, null, null, 1460493081, 1094348356, 1181016291, 1437219675, 17448597, "SRX392057", "SRS515268", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.93308, 0.90255, 0.16256, 0.15653, 0.78307, 0.78675, 0.67868, 0.6873, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37260, "SRR1049957", "SRX392057", "SRS515268", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Treated biological replicate 3", "GSM1289435", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "Treated biological replicate 3", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "GSM1289435", "GSM1289435: Treated biological replicate 3; Danio rerio; RNA Seq", "GSM1289435", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_TF13_index23_GAGTGG_L001_R2.fastq.gz TFJN03_TF13_index23_GAGTGG_L001_R1.fastq.gz", "fastq fastq", 4688668200.0, 23443341.0, "GSM1289435 r2", "0:100 1:100", "A:1307237255;C:986117281;G:1055375359;T:1309868568;N:30069737", 100, 100, null, null, 1307237255, 986117281, 1055375359, 1309868568, 30069737, "SRX392057", "SRS515268", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.9283, 0.89132, 0.1621, 0.15554, 0.78163, 0.78855, 0.6781, 0.67998, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37261, "SRR1049954", "SRX392056", "SRS515267", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Treated biological replicate 2", "GSM1289434", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "Treated biological replicate 2", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "GSM1289434", "GSM1289434: Treated biological replicate 2; Danio rerio; RNA Seq", "GSM1289434", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_11_index21_GTTTCG_L008_R1.fastq.gz TFJN03_11_index21_GTTTCG_L008_R2.fastq.gz", "fastq fastq", 5609167200.0, 28045836.0, "GSM1289434 r1", "0:100 1:100", "A:1450253696;C:1301075598;G:1404930257;T:1434234288;N:18673361", 100, 100, null, null, 1450253696, 1301075598, 1404930257, 1434234288, 18673361, "SRX392056", "SRS515267", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.9355, 0.90787, 0.15031, 0.14637, 0.84238, 0.84459, 0.6262, 0.62238, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37262, "SRR1049955", "SRX392056", "SRS515267", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Treated biological replicate 2", "GSM1289434", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "Treated biological replicate 2", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "GSM1289434", "GSM1289434: Treated biological replicate 2; Danio rerio; RNA Seq", "GSM1289434", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_TF11_index21_GTTTCG_L001_R1.fastq.gz TFJN03_TF11_index21_GTTTCG_L001_R2.fastq.gz", "fastq fastq", 5193245800.0, 25966229.0, "GSM1289434 r2", "0:100 1:100", "A:1326311647;C:1205502607;G:1294551721;T:1334160834;N:32718991", 100, 100, null, null, 1326311647, 1205502607, 1294551721, 1334160834, 32718991, "SRX392056", "SRS515267", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.93101, 0.89734, 0.15109, 0.14654, 0.84106, 0.84695, 0.59767, 0.60125, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37263, "SRR1049952", "SRX392055", "SRS515266", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Treated biological replicate 1", "GSM1289433", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "Treated biological replicate 1", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "GSM1289433", "GSM1289433: Treated biological replicate 1; Danio rerio; RNA Seq", "GSM1289433", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_9_index19_GTGAAA_L008_R2.fastq.gz TFJN03_9_index19_GTGAAA_L008_R1.fastq.gz", "fastq fastq", 6350027200.0, 31750136.0, "GSM1289433 r1", "0:100 1:100", "A:1818353364;C:1327246344;G:1460644244;T:1722864561;N:20918687", 100, 100, null, null, 1818353364, 1327246344, 1460644244, 1722864561, 20918687, "SRX392055", "SRS515266", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.92989, 0.89149, 0.12053, 0.11545, 0.82479, 0.82919, 0.72065, 0.69829, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37264, "SRR1049953", "SRX392055", "SRS515266", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Treated biological replicate 1", "GSM1289433", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "Treated biological replicate 1", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 \u00b5M gallein", "GSM1289433", "GSM1289433: Treated biological replicate 1; Danio rerio; RNA Seq", "GSM1289433", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_TF9_index19_GTGAAA_L001_R2.fastq.gz TFJN03_TF9_index19_GTGAAA_L001_R1.fastq.gz", "fastq fastq", 5477198400.0, 27385992.0, "GSM1289433 r2", "0:100 1:100", "A:1526066704;C:1150303729;G:1233326927;T:1532243060;N:35257980", 100, 100, null, null, 1526066704, 1150303729, 1233326927, 1532243060, 35257980, "SRX392055", "SRS515266", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.92412, 0.87983, 0.1198, 0.11437, 0.81874, 0.82546, 0.73064, 0.72533, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37265, "SRR1049950", "SRX392054", "SRS515265", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Control biological replicate 3", "GSM1289432", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "Control biological replicate 3", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "GSM1289432", "GSM1289432: Control biological replicate 3; Danio rerio; RNA Seq", "GSM1289432", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_5_index15_ATGTCA_L008_R1.fastq.gz TFJN03_5_index15_ATGTCA_L008_R2.fastq.gz", "fastq fastq", 5273558800.0, 26367794.0, "GSM1289432 r1", "0:100 1:100", "A:1477792186;C:1115051166;G:1194650762;T:1468545239;N:17519447", 100, 100, null, null, 1477792186, 1115051166, 1194650762, 1468545239, 17519447, "SRX392054", "SRS515265", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.92708, 0.88737, 0.10723, 0.10296, 0.77772, 0.78033, 0.68667, 0.68521, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37266, "SRR1049951", "SRX392054", "SRS515265", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Control biological replicate 3", "GSM1289432", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "Control biological replicate 3", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "GSM1289432", "GSM1289432: Control biological replicate 3; Danio rerio; RNA Seq", "GSM1289432", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_TF5_index15_ATGTCA_L001_R1.fastq.gz TFJN03_TF5_index15_ATGTCA_L001_R2.fastq.gz", "fastq fastq", 4863193200.0, 24315966.0, "GSM1289432 r2", "0:100 1:100", "A:1346938283;C:1025346554;G:1093434022;T:1366438219;N:31036122", 100, 100, null, null, 1346938283, 1025346554, 1093434022, 1366438219, 31036122, "SRX392054", "SRS515265", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.92292, 0.87537, 0.10864, 0.10333, 0.77388, 0.78088, 0.69247, 0.68232, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37267, "SRR1049948", "SRX392053", "SRS515264", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Control biological replicate 2", "GSM1289431", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "Control biological replicate 2", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "GSM1289431", "GSM1289431: Control biological replicate 2; Danio rerio; RNA Seq", "GSM1289431", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_3_index13_AGTCAA_L008_R1.fastq.gz TFJN03_3_index13_AGTCAA_L008_R2.fastq.gz", "fastq fastq", 6232049200.0, 31160246.0, "GSM1289431 r1", "0:100 1:100", "A:1766119095;C:1306322138;G:1392793942;T:1746336195;N:20477830", 100, 100, null, null, 1766119095, 1306322138, 1392793942, 1746336195, 20477830, "SRX392053", "SRS515264", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.92673, 0.8984, 0.12936, 0.12463, 0.7517, 0.75388, 0.70192, 0.70136, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37268, "SRR1049949", "SRX392053", "SRS515264", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Control biological replicate 2", "GSM1289431", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "Control biological replicate 2", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "GSM1289431", "GSM1289431: Control biological replicate 2; Danio rerio; RNA Seq", "GSM1289431", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_TF3_index13_AGTCAA_L001_R1.fastq.gz TFJN03_TF3_index13_AGTCAA_L001_R2.fastq.gz", "fastq fastq", 5637087000.0, 28185435.0, "GSM1289431 r2", "0:100 1:100", "A:1581520083;C:1176550014;G:1249525371;T:1593435949;N:36055583", 100, 100, null, null, 1581520083, 1176550014, 1249525371, 1593435949, 36055583, "SRX392053", "SRS515264", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.92369, 0.88925, 0.12975, 0.12262, 0.75037, 0.75771, 0.71186, 0.71148, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37269, "SRR1049946", "SRX392052", "SRS515263", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Control biological replicate 1", "GSM1289430", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "Control biological replicate 1", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "GSM1289430", "GSM1289430: Control biological replicate 1; Danio rerio; RNA Seq", "GSM1289430", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289430", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_1_index11_GGCTAC_L008_R1.fastq.gz TFJN03_1_index11_GGCTAC_L008_R2.fastq.gz", "fastq fastq", 5777615200.0, 28888076.0, "GSM1289430 r1", "0:100 1:100", "A:1594355339;C:1261845006;G:1365822147;T:1536556082;N:19036626", 100, 100, null, null, 1594355339, 1261845006, 1365822147, 1536556082, 19036626, "SRX392052", "SRS515263", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.93871, 0.90851, 0.10423, 0.0988, 0.79401, 0.79768, 0.61422, 0.68712, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [37270, "SRR1049947", "SRX392052", "SRS515263", "SRP034166", "PRJNA231739", "Silencing of odorant receptor gene expression by G protein \u00df? signaling ensures the expression of one odorant receptor per olfactory sensory neuron", "GSE53334", "Transcriptome Analysis", "Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes  reflecting an exquisite mode of gene regulation. In one model  once an odorant receptor is chosen for expression  other receptor genes are suppressed by a negative feedback mechanism  ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure  however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover  we show that signaling through G protein \u00df? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes  and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples", null, "pubmed:24559675;pubmed:25150836", null, "Control biological replicate 1", "GSM1289430", null, "tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "Control biological replicate 1", "Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference  defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences  using TopHat v. 2.0.4  supplying the Ensembl GTF annotation through the  G option Gene level read counts were generated using the htseq count python script in the \"union\" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample", "Olfactory sensory neuron", "At 16 hpf 20 hpf  embryos were treated with 100 \u00b5M gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours.  Heads of 5  dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at  80oC", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.", "tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:DMSO", "GSM1289430", "GSM1289430: Control biological replicate 1; Danio rerio; RNA Seq", "GSM1289430", null, "1", "Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies  cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer\u2019s IntegenX  Inc. protocols.", "GEO Accession:GSM1289430", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP034166", null, null, "TFJN03_TF1_index11_GGCTAC_L001_R2.fastq.gz TFJN03_TF1_index11_GGCTAC_L001_R1.fastq.gz", "fastq fastq", 5192582000.0, 25962910.0, "GSM1289430 r2", "0:100 1:100", "A:1404101823;C:1135531797;G:1211215338;T:1408860806;N:32872236", 100, 100, null, null, 1404101823, 1135531797, 1211215338, 1408860806, 32872236, "SRX392052", "SRS515263", "SRA116880", "GEO", "University of California, Berkeley", 2, 0.93504, 0.89822, 0.10499, 0.09971, 0.78904, 0.79608, 0.62078, 0.68958, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-12-15", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [55530, "SRR10527609", "SRX7212100", "SRS5714969", "SRP233088", "PRJNA591638", "dmh4/+ severe scoliosis brain RNA sequencing", "PRJNA591638", "Other", "RNA sequencing preformed on brains dissected from dmh4/+ zebrafish with severe scoliosis to identify gene expression involved in idiopathic scoliosis.", null, null, null, null, "wildtype", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:whole brain|phenotype:straight spine|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of scoliotic zebrafish brains: wildtype sibling with straight spine", "wt H", "wt H", "3 brains were pooled from 21 dpf fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP233088", null, "loader:fastq load.py", "wt_CPGFP_3brains_H_R1.fastq.gz wt_CPGFP_3brains_H_R2.fastq.gz", "fastq fastq", 22816701936.0, 90542468.0, "wt CPGFP 3brains H R1.fastq.gz", "0:126 1:126", "A:6403495683;C:4996055352;G:4989237508;T:6421208778;N:6704615", 126, 126, null, null, 6403495683, 4996055352, 4989237508, 6421208778, 6704615, "SRX7212100", "SRS5714969", "SRA1002469", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.95628, 0.95875, 0.14601, 0.14507, 0.69035, 0.69065, 0.48565, 0.48768, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", 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