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181 rows where devstage_curation = "Multi-stage" and tissue_curation = "Brain"

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technology 3

experiment.library_source 2

experiment.library_selection 2

experiment.library_layout 2

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 181 ✖

experiment.platform 1

experiment.library_strategy 1

devstage_curation 1

  • Multi-stage · 181 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29047 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–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß 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 ß 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.   pubmed:39526957   WT brain 3 GSM7924152   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® 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°C. 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°C 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® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474986   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     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   Canada 2023-11-29 Multi-stage Multi-stage Brain Nervous System
29048 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–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß 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 ß 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.   pubmed:39526957   WT brain 2 GSM7924151   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® 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°C. 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°C 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® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474986   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     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   Canada 2023-11-29 Multi-stage Multi-stage Brain Nervous System
29049 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–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß 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 ß 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.   pubmed:39526957   WT brain 1 GSM7924150   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® 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°C. 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°C 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® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474986   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     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   Canada 2023-11-29 Multi-stage Multi-stage Brain Nervous System
29050 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–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß 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 ß 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.   pubmed:39526957   itgavKO brain 3 GSM7924149   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® 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°C. 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°C 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® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474986   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     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   Canada 2023-11-29 Multi-stage Multi-stage Brain Nervous System
29051 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–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß 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 ß 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.   pubmed:39526957   itgavKO brain 2 GSM7924148   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® 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°C. 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°C 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® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474986   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     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   Canada 2023-11-29 Multi-stage Multi-stage Brain Nervous System
29052 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–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß 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 ß 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.   pubmed:39526957   itgavKO brain 1 GSM7924147   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® 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°C. 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°C 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® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474986   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     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   Canada 2023-11-29 Multi-stage Multi-stage Brain Nervous System
29059 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.       rnaset2 scr sham C3 C3   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29060 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.       rnaset2 scr sham C2 C2   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     1397754308 1184093732 1220417954 1372707855 7851 SRX22702841 SRS19695450 SRA1760882 University of York|Biology University of York 2 0.94447 0.94375 0.11969 0.11666 0.68885 0.68956 0.49127 0.48884 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29061 29061 SRR27010034 SRX22702840 SRS19695449 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.       WT irf8 sham B6 B6   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:B6|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29062 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.       WT irf8 sham B4 B4   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     B4_R1_001.fastq.gz B4_R2_001.fastq.gz fastq fastq 4670850600.0 15569502.0 B4 R1 001.fastq.gz 0:150 1:150 A:1265811314;C:1065724201;G:1097798356;T:1241510089;N:6640 150 150     1265811314 1065724201 1097798356 1241510089 6640 SRX22702839 SRS19695448 SRA1760882 University of York|Biology University of York 2 0.94547 0.94517 0.11922 0.11549 0.68968 0.69029 0.48585 0.48669 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29063 29063 SRR27010036 SRX22702838 SRS19695446 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.       WT irf8 sham B3 B3   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29064 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.       WT irf8 sham B2 B2   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29065 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.       WT scr sham A9 A9   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29066 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.       rnaset2 irf8 transplanted visible cells G8 G8   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29067 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.       rnaset2 irf8 transplanted visible cells G5 G5   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                 RNA seq of zebrafish: brain G5 G5 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     G5_R2_001.fastq.gz G5_R1_001.fastq.gz fastq fastq 8086012500.0 26953375.0 G5 R1 001.fastq.gz 0:150 1:150 A:2209424775;C:1827141351;G:1886144200;T:2163290263;N:11911 150 150     2209424775 1827141351 1886144200 2163290263 11911 SRX22702834 SRS19695443 SRA1760882 University of York|Biology University of York 2 0.94005 0.94009 0.13869 0.13535 0.68874 0.68876 0.49518 0.49562 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29068 29068 SRR27010041 SRX22702833 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.       rnaset2 irf8 transplanted visible cells G4 G4   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     G4_R2_001.fastq.gz G4_R1_001.fastq.gz fastq fastq 11168836800.0 37229456.0 G4 R1 001.fastq.gz 0:150 1:150 A:3056935929;C:2522420915;G:2603785258;T:2985677785;N:16913 150 150     3056935929 2522420915 2603785258 2985677785 16913 SRX22702833 SRS19695442 SRA1760882 University of York|Biology University of York 2 0.94154 0.94245 0.13303 0.12991 0.68298 0.68428 0.49109 0.49258 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29069 29069 SRR27010042 SRX22702832 SRS19695441 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.       rnaset2 irf8 transplanted visible cells G1 G1   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     1832990297 1535916761 1572331210 1804054965 10267 SRX22702832 SRS19695441 SRA1760882 University of York|Biology University of York 2 0.9424 0.94298 0.12822 0.12534 0.68775 0.68854 0.4869 0.48958 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29070 29070 SRR27010043 SRX22702831 SRS19695440 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.       rnaset2 scr transplanted non visible cells F5 F5   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:F5|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain F5 F5 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     F5_R1_001.fastq.gz F5_R2_001.fastq.gz fastq fastq 6464113800.0 21547046.0 F5 R1 001.fastq.gz 0:150 1:150 A:1773652408;C:1452872569;G:1501709404;T:1735869784;N:9635 150 150     1773652408 1452872569 1501709404 1735869784 9635 SRX22702831 SRS19695440 SRA1760882 University of York|Biology University of York 2 0.93953 0.93885 0.13889 0.13589 0.68448 0.68568 0.49419 0.49486 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29071 29071 SRR27010044 SRX22702830 SRS19695439 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.       rnaset2 scr transplanted non visible cells F4 F4   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:F4|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain F4 F4 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     F4_R1_001.fastq.gz F4_R2_001.fastq.gz fastq fastq 7547491800.0 25158306.0 F4 R1 001.fastq.gz 0:150 1:150 A:2043215956;C:1726123019;G:1778767478;T:1999373636;N:11711 150 150     2043215956 1726123019 1778767478 1999373636 11711 SRX22702830 SRS19695439 SRA1760882 University of York|Biology University of York 2 0.94829 0.94765 0.11775 0.11477 0.68682 0.68783 0.48624 0.49294 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29072 29072 SRR27010045 SRX22702829 SRS19695437 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.       rnaset2 scr transplanted non visible cells F3 F3   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:F3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain F3 F3 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     F3_R1_001.fastq.gz F3_R2_001.fastq.gz fastq fastq 7796779800.0 25989266.0 F3 R1 001.fastq.gz 0:150 1:150 A:2138759764;C:1759352855;G:1808448742;T:2090206548;N:11891 150 150     2138759764 1759352855 1808448742 2090206548 11891 SRX22702829 SRS19695437 SRA1760882 University of York|Biology University of York 2 0.94125 0.9421 0.13575 0.13224 0.69307 0.69469 0.4862 0.48802 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29073 29073 SRR27010046 SRX22702828 SRS19695438 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.       WT scr sham A4 A4   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:A4|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain A4 A4 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     A4_R1_001.fastq.gz A4_R2_001.fastq.gz fastq fastq 6954570300.0 23181901.0 A4 R1 001.fastq.gz 0:150 1:150 A:1888329109;C:1587042583;G:1627429667;T:1851758485;N:10456 150 150     1888329109 1587042583 1627429667 1851758485 10456 SRX22702828 SRS19695438 SRA1760882 University of York|Biology University of York 2 0.94568 0.94593 0.11814 0.1154 0.69171 0.69161 0.49417 0.49201 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29074 29074 SRR27010047 SRX22702827 SRS19695436 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.       rnaset2 scr transplanted non visible cells F2 F2   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:F2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain F2 F2 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     F2_R2_001.fastq.gz F2_R1_001.fastq.gz fastq fastq 7064875200.0 23549584.0 F2 R1 001.fastq.gz 0:150 1:150 A:1909747576;C:1617295332;G:1667877510;T:1869944260;N:10522 150 150     1909747576 1617295332 1667877510 1869944260 10522 SRX22702827 SRS19695436 SRA1760882 University of York|Biology University of York 2 0.94737 0.94827 0.10024 0.09772 0.69057 0.69146 0.49402 0.49924 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29075 29075 SRR27010048 SRX22702826 SRS19695435 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.       rnaset2 scr transplanted visible cells E5 E5   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:E5|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain E5 E5 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     E5_R1_001.fastq.gz E5_R2_001.fastq.gz fastq fastq 9245045700.0 30816819.0 E5 R1 001.fastq.gz 0:150 1:150 A:2541240585;C:2078884464;G:2136224399;T:2488682323;N:13929 150 150     2541240585 2078884464 2136224399 2488682323 13929 SRX22702826 SRS19695435 SRA1760882 University of York|Biology University of York 2 0.93981 0.93963 0.14018 0.13679 0.68544 0.68647 0.48749 0.49123 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29076 29076 SRR27010049 SRX22702825 SRS19695434 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.       rnaset2 scr transplanted visible cells E4 E4   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:E4|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain E4 E4 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     E4_R1_001.fastq.gz E4_R2_001.fastq.gz fastq fastq 9413066700.0 31376889.0 E4 R1 001.fastq.gz 0:150 1:150 A:2556541599;C:2141951710;G:2209637678;T:2504921319;N:14394 150 150     2556541599 2141951710 2209637678 2504921319 14394 SRX22702825 SRS19695434 SRA1760882 University of York|Biology University of York 2 0.93966 0.94056 0.13191 0.13025 0.6845 0.68458 0.48562 0.48775 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29077 29077 SRR27010050 SRX22702824 SRS19695433 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.       rnaset2 scr transplanted visible cells E3 E3   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:E3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain E3 E3 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     E3_R1_001.fastq.gz E3_R2_001.fastq.gz fastq fastq 7964919000.0 26549730.0 E3 R1 001.fastq.gz 0:150 1:150 A:2160541660;C:1817481684;G:1869600595;T:2117282750;N:12311 150 150     2160541660 1817481684 1869600595 2117282750 12311 SRX22702824 SRS19695433 SRA1760882 University of York|Biology University of York 2 0.94418 0.94436 0.12381 0.12155 0.69043 0.69244 0.49578 0.49427 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29078 29078 SRR27010051 SRX22702823 SRS19695432 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.       rnaset2 irf8 sham D7 D7   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:D7|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain D7 D7 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     D7_R1_001.fastq.gz D7_R2_001.fastq.gz fastq fastq 9187165200.0 30623884.0 D7 R1 001.fastq.gz 0:150 1:150 A:2491532789;C:2097618431;G:2151100077;T:2446900236;N:13667 150 150     2491532789 2097618431 2151100077 2446900236 13667 SRX22702823 SRS19695432 SRA1760882 University of York|Biology University of York 2 0.94299 0.94212 0.11906 0.11545 0.68306 0.68548 0.49177 0.49121 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29079 29079 SRR27010052 SRX22702822 SRS19695430 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.       rnaset2 irf8 sham D6 D6   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:D6|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain D6 D6 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     D6_R1_001.fastq.gz D6_R2_001.fastq.gz fastq fastq 5879800500.0 19599335.0 D6 R1 001.fastq.gz 0:150 1:150 A:1605109827;C:1329412433;G:1368575434;T:1576693845;N:8961 150 150     1605109827 1329412433 1368575434 1576693845 8961 SRX22702822 SRS19695430 SRA1760882 University of York|Biology University of York 2 0.94062 0.94076 0.12643 0.12267 0.67959 0.68079 0.4953 0.49028 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29080 29080 SRR27010053 SRX22702821 SRS19695431 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.       rnaset2 irf8 sham D5 D5   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:D5|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain D5 D5 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     D5_R1_001.fastq.gz D5_R2_001.fastq.gz fastq fastq 6561881400.0 21872938.0 D5 R1 001.fastq.gz 0:150 1:150 A:1784761040;C:1494553700;G:1531680450;T:1750875924;N:10286 150 150     1784761040 1494553700 1531680450 1750875924 10286 SRX22702821 SRS19695431 SRA1760882 University of York|Biology University of York 2 0.94309 0.94372 0.12249 0.11939 0.6896 0.69126 0.4916 0.48496 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29081 29081 SRR27010054 SRX22702820 SRS19695429 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.       rnaset2 irf8 sham D2 D2   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:D2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain D2 D2 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     D2_R1_001.fastq.gz D2_R2_001.fastq.gz fastq fastq 6654501900.0 22181673.0 D2 R1 001.fastq.gz 0:150 1:150 A:1814773421;C:1511191953;G:1552895235;T:1775631113;N:10178 150 150     1814773421 1511191953 1552895235 1775631113 10178 SRX22702820 SRS19695429 SRA1760882 University of York|Biology University of York 2 0.94117 0.94183 0.13042 0.12757 0.68578 0.68747 0.49634 0.49724 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29082 29082 SRR27010055 SRX22702819 SRS19695428 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.       rnaset2 scr sham C5 C5   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:C5|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: brain C5 C5 RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     C5_R2_001.fastq.gz C5_R1_001.fastq.gz fastq fastq 6839917500.0 22799725.0 C5 R1 001.fastq.gz 0:150 1:150 A:1862202751;C:1544536021;G:1599909841;T:1833258970;N:9917 150 150     1862202751 1544536021 1599909841 1833258970 9917 SRX22702819 SRS19695428 SRA1760882 University of York|Biology University of York 2 0.94311 0.9429 0.12484 0.12074 0.68899 0.69077 0.49108 0.49366 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29083 29083 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.       rnaset2 scr sham C4 C4   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     C4_R1_001.fastq.gz C4_R2_001.fastq.gz fastq fastq 6814278600.0 22714262.0 C4 R1 001.fastq.gz 0:150 1:150 A:1829280895;C:1574717969;G:1616401528;T:1793867756;N:10452 150 150     1829280895 1574717969 1616401528 1793867756 10452 SRX22702818 SRS19695427 SRA1760882 University of York|Biology University of York 2 0.94942 0.95087 0.09719 0.09395 0.69445 0.69507 0.49061 0.49227 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29084 29084 SRR27010057 SRX22702817 SRS19695425 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.       WT scr sham A2 A2   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29085 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.       WT scr sham A1 A1   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                 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     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP475263     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     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   United Kingdom 2023-12-01 Multi-stage Multi-stage Brain Nervous System
29820 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 f…   pubmed:38519480   non syn 19 1 GSM8012748   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     895917474 489293250 641228744 1091230120 49512 SRX23170207 SRS20119604 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29821 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 f…   pubmed:38519480   non syn 10 1 GSM8012747   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1317989544 684597236 860222705 1635432063 163052 SRX23170206 SRS20119603 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29822 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 f…   pubmed:38519480   non syn 22 GSM8012746   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     717072489 371259220 487966761 874532663 52167 SRX23170205 SRS20119602 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29823 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 f…   pubmed:38519480   non syn 18 GSM8012745   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     707890019 383065085 518277437 872001065 41794 SRX23170204 SRS20119601 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29824 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 f…   pubmed:38519480   non syn 17 GSM8012744   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     523356732 311424242 413587608 654191534 15584 SRX23170203 SRS20119600 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29825 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 f…   pubmed:38519480   non syn 15 GSM8012743   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     764042895 415507565 493804628 971168170 44842 SRX23170202 SRS20119599 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29826 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 f…   pubmed:38519480   non syn 13 GSM8012742   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     981997806 535742678 672084090 1154576135 10691 SRX23170201 SRS20119598 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29827 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 f…   pubmed:38519480   non syn 10 GSM8012741   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1442162587 766015788 971257296 1801275462 180467 SRX23170200 SRS20119597 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29828 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 f…   pubmed:38519480   non syn 6 GSM8012740   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     971399150 550458386 698401196 1166169792 11076 SRX23170199 SRS20119596 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29829 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 f…   pubmed:38519480   non syn 5 GSM8012739   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1874497306 1098473614 1392771685 2328388616 243679 SRX23170198 SRS20119595 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29830 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 f…   pubmed:38519480   syn 22 GSM8012738   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     743952075 396567355 527169920 909228265 44885 SRX23170197 SRS20119594 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29831 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 f…   pubmed:38519480   syn 21 GSM8012737   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     906029209 480116580 641470237 1111517808 66166 SRX23170196 SRS20119593 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29832 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 f…   pubmed:38519480   syn 20 GSM8012736   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1288150411 745135993 1003148625 1564941023 124448 SRX23170195 SRS20119592 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29833 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 f…   pubmed:38519480   syn 16 GSM8012735   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     714860453 407690072 525572866 918632205 21304 SRX23170194 SRS20119591 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29834 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 f…   pubmed:38519480   syn 14 1 GSM8012734   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1155899190 576621004 728773344 1380391692 12770 SRX23170193 SRS20119590 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29835 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 f…   pubmed:38519480   syn 9 GSM8012733   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1501566241 777725902 1012263041 1849766543 175473 SRX23170192 SRS20119589 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29836 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 f…   pubmed:38519480   syn 6 GSM8012732   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1017036453 585222109 725483108 1314599102 9928 SRX23170191 SRS20119588 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29837 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 f…   pubmed:38519480   syn 5 GSM8012731   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1001098139 530696334 690506502 1224479197 84228 SRX23170190 SRS20119587 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29838 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 f…   pubmed:38519480   syn 4 1 GSM8012730   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     1468672385 876455469 1192232488 1925328687 103971 SRX23170189 SRS20119586 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
29839 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 f…   pubmed:38519480   syn 4 GSM8012729   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP483288     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     516279078 299222574 422785519 652613922 26807 SRX23170188 SRS20119585 SRA1784161 Neuroscience, School of Medcine, Tongji University, 42508444-9 Neuroscience, School of Medcine, Tongji University, 42508444-9                       T B mate1 technical by mapping diff illumina nextseq_v2 unknown cdna_unspecified trueseq bulk unknown unknown   China 2024-01-11 Multi-stage Multi-stage Brain Nervous System
30256 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.       Late born vestibular neurons replicate 2 GSM8038041   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30257 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.       Late born vestibular neurons replicate 2 GSM8038041   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30258 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.       Late born vestibular neurons replicate 2 GSM8038041   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30259 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.       Late born vestibular neurons replicate 2 GSM8038041   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30260 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.       Early born vestibular neurons replicate 1 GSM8038040   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30261 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.       Early born vestibular neurons replicate 1 GSM8038040   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30262 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.       Early born vestibular neurons replicate 1 GSM8038040   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30263 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.       Early born vestibular neurons replicate 1 GSM8038040   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30264 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.       All vestibular neurons replicate 3 GSM8038039   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30265 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.       All vestibular neurons replicate 3 GSM8038039   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30266 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.       All vestibular neurons replicate 3 GSM8038039   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30267 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.       All vestibular neurons replicate 3 GSM8038039   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30268 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.       All vestibular neurons replicate 2 GSM8038038   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30269 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.       All vestibular neurons replicate 2 GSM8038038   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30270 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.       All vestibular neurons replicate 2 GSM8038038   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30271 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.       All vestibular neurons replicate 2 GSM8038038   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30272 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.       All vestibular neurons replicate 1 GSM8038037   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30273 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.       All vestibular neurons replicate 1 GSM8038037   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30274 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.       All vestibular neurons replicate 1 GSM8038037   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
30275 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.       All vestibular neurons replicate 1 GSM8038037   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   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   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486180   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                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-26 Multi-stage Multi-stage Brain Nervous System
33194 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 methylom…   pubmed:39742644   IPP 120hpf brain replicate4 GSM8399288   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33195 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 methylom…   pubmed:39742644   IPP 120hpf brain replicate3 GSM8399287   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33196 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 methylom…   pubmed:39742644   IPP 120hpf brain replicate2 GSM8399286   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33197 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 methylom…   pubmed:39742644   IPP 120hpf brain replicate1 GSM8399285   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33198 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 methylom…   pubmed:39742644   DMSO 120hpf brain replicate4 GSM8399284   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33199 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 methylom…   pubmed:39742644   DMSO 120hpf brain replicate3 GSM8399283   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33200 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 methylom…   pubmed:39742644   DMSO 120hpf brain replicate2 GSM8399282   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
33201 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 methylom…   pubmed:39742644   DMSO 120hpf brain replicate1 GSM8399281   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     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     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   United States 2024-07-16 Multi-stage Multi-stage Brain Nervous System
34088 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 µg/L to 1000 µg/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 µg/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 tr…       6PPD 3 GSM8582553   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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. 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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539617     6PPD3head_Clean_Data1.fq.gz 6PPD3head_Clean_Data2.fq.gz fastq fastq 5643201065.0 19058349.0 GSM8582553 r1                       SRX26432306 SRS22949546 SRA1994053 Guizhou Medical University Guizhou Medical University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-10-19 Multi-stage Embryo Brain Nervous System
34089 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 µg/L to 1000 µg/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 µg/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 tr…       6PPD 2 GSM8582552   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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. 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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539617     6PPD2head_Clean_Data1.fq.gz 6PPD2head_Clean_Data2.fq.gz fastq fastq 6184525960.0 20877930.0 GSM8582552 r1                       SRX26432305 SRS22949545 SRA1994053 Guizhou Medical University Guizhou Medical University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-10-19 Multi-stage Embryo Brain Nervous System
34090 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 µg/L to 1000 µg/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 µg/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 tr…       6PPD 1 GSM8582551   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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. 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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539617     6PPD1head_Clean_Data1.fq.gz 6PPD1head_Clean_Data2.fq.gz fastq fastq 5412472152.0 18274114.0 GSM8582551 r1                       SRX26432304 SRS22949544 SRA1994053 Guizhou Medical University Guizhou Medical University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-10-19 Multi-stage Embryo Brain Nervous System
34091 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 µg/L to 1000 µg/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 µg/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 tr…       Con 3 GSM8582550   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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. 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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539617     Con3head_Clean_Data1.fq.gz Con3head_Clean_Data2.fq.gz fastq fastq 6118959402.0 20641047.0 GSM8582550 r1                       SRX26432303 SRS22949543 SRA1994053 Guizhou Medical University Guizhou Medical University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-10-19 Multi-stage Embryo Brain Nervous System
34092 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 µg/L to 1000 µg/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 µg/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 tr…       Con 2 GSM8582549   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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. 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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539617     Con2head_Clean_Data1.fq.gz Con2head_Clean_Data2.fq.gz fastq fastq 5778620515.0 19519984.0 GSM8582549 r1                       SRX26432302 SRS22949542 SRA1994053 Guizhou Medical University Guizhou Medical University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-10-19 Multi-stage Embryo Brain Nervous System
34093 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 µg/L to 1000 µg/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 µg/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 tr…       Con 1 GSM8582548   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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. 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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539617     Con1head_Clean_Data1.fq.gz Con1head_Clean_Data2.fq.gz fastq fastq 5538973366.0 18707123.0 GSM8582548 r1                       SRX26432301 SRS22949541 SRA1994053 Guizhou Medical University Guizhou Medical University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-10-19 Multi-stage Embryo Brain Nervous System
37259 37259 SRR1049956 SRX392057 SRS515268 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Treated biological replicate 3 GSM1289435   tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 µM 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 µM 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’s 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 µM gallein GSM1289435 GSM1289435: Treated biological replicate 3; Danio rerio; RNA Seq GSM1289435   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’s IntegenX Inc. protocols. GEO Accession:GSM1289435 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37260 37260 SRR1049957 SRX392057 SRS515268 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Treated biological replicate 3 GSM1289435   tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 µM 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 µM 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’s 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 µM gallein GSM1289435 GSM1289435: Treated biological replicate 3; Danio rerio; RNA Seq GSM1289435   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’s IntegenX Inc. protocols. GEO Accession:GSM1289435 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37261 37261 SRR1049954 SRX392056 SRS515267 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Treated biological replicate 2 GSM1289434   tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 µM 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 µM 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’s 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 µM gallein GSM1289434 GSM1289434: Treated biological replicate 2; Danio rerio; RNA Seq GSM1289434   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’s IntegenX Inc. protocols. GEO Accession:GSM1289434 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37262 37262 SRR1049955 SRX392056 SRS515267 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Treated biological replicate 2 GSM1289434   tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 µM 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 µM 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’s 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 µM gallein GSM1289434 GSM1289434: Treated biological replicate 2; Danio rerio; RNA Seq GSM1289434   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’s IntegenX Inc. protocols. GEO Accession:GSM1289434 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37263 37263 SRR1049952 SRX392055 SRS515266 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Treated biological replicate 1 GSM1289433   tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 µM 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 µM 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’s 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 µM gallein GSM1289433 GSM1289433: Treated biological replicate 1; Danio rerio; RNA Seq GSM1289433   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’s IntegenX Inc. protocols. GEO Accession:GSM1289433 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37264 37264 SRR1049953 SRX392055 SRS515266 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Treated biological replicate 1 GSM1289433   tissue:Olfactory sensory neuron|tansgenic line:OMP Gal4 transgenic zebrafish|cell sorting:GFP +|agent:100 µM 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 µM 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’s 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 µM gallein GSM1289433 GSM1289433: Treated biological replicate 1; Danio rerio; RNA Seq GSM1289433   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’s IntegenX Inc. protocols. GEO Accession:GSM1289433 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37265 37265 SRR1049950 SRX392054 SRS515265 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Control biological replicate 3 GSM1289432   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 µM 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’s 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   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’s IntegenX Inc. protocols. GEO Accession:GSM1289432 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37266 37266 SRR1049951 SRX392054 SRS515265 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Control biological replicate 3 GSM1289432   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 µM 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’s 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   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’s IntegenX Inc. protocols. GEO Accession:GSM1289432 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37267 37267 SRR1049948 SRX392053 SRS515264 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Control biological replicate 2 GSM1289431   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 µM 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’s 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   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’s IntegenX Inc. protocols. GEO Accession:GSM1289431 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37268 37268 SRR1049949 SRX392053 SRS515264 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Control biological replicate 2 GSM1289431   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 µM 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’s 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   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’s IntegenX Inc. protocols. GEO Accession:GSM1289431 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37269 37269 SRR1049946 SRX392052 SRS515263 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Control biological replicate 1 GSM1289430   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 µM 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’s 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   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’s IntegenX Inc. protocols. GEO Accession:GSM1289430 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
37270 37270 SRR1049947 SRX392052 SRS515263 SRP034166 PRJNA231739 Silencing of odorant receptor gene expression by G protein ß? 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 ß? 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   pubmed:24559675;pubmed:25150836   Control biological replicate 1 GSM1289430   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 µM 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’s 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   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’s IntegenX Inc. protocols. GEO Accession:GSM1289430 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP034166     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     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   United States 2013-12-15 Multi-stage Multi-stage Brain Nervous System
55530 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.         wildtype   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP233088   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     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   Canada 2019-11-27 Multi-stage Multi-stage Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;