{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"smartseq\" and tissue_curation = \"Brain\"", "rows": [[10237, "ERR7131169", "ERX6698608", "ERS8070397", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F8 Nega", "SAMEA10418613", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418613|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F8 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 8|organism part:olfactory bulb|sample name:E MTAB 11083:F8 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F8 Nega s", "F8 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. 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Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F8 Nega", "SAMEA10418613", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418613|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F8 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 8|organism part:olfactory bulb|sample name:E MTAB 11083:F8 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F8 Nega s", "F8 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F22-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTAAGCCT_L007_R1_001.fastq.gz", "fastq", 661103769.0, 12962819.0, "E MTAB 11083:2874F22 2 210715 D00404 0538 BCD91CANXX TCGACGTC CTAAGCCT L007", "0:51 1:0", "A:174223249;C:153223284;G:148276805;T:185335092;N:45339", 51, 0, null, null, 174223249, 153223284, 148276805, 185335092, 45339, "ERX6698608", "ERS8070397", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.78539, null, 0.15054, null, 0.70897, null, 0.5322, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10239, "ERR7131167", "ERX6698607", "ERS8070396", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F8 mCherry GFP", "SAMEA10418612", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418612|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F8 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 8|organism part:olfactory bulb|sample name:E MTAB 11083:F8 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F8 mCherry GFP s", "F8 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F24-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-TCTCTCCG_L006_R1_001.fastq.gz", "fastq", 693183636.0, 13591836.0, "E MTAB 11083:2874F24 1 210715 D00404 0538 BCD91CANXX TCGACGTC TCTCTCCG L006", "0:51 1:0", "A:183977687;C:159275153;G:153149826;T:196732022;N:48948", 51, 0, null, null, 183977687, 159275153, 153149826, 196732022, 48948, "ERX6698607", "ERS8070396", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.68942, null, 0.15593, null, 0.75828, null, 0.51858, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10240, "ERR7131168", "ERX6698607", "ERS8070396", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F8 mCherry GFP", "SAMEA10418612", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418612|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F8 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 8|organism part:olfactory bulb|sample name:E MTAB 11083:F8 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F8 mCherry GFP s", "F8 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F24-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-TCTCTCCG_L007_R1_001.fastq.gz", "fastq", 696648678.0, 13659778.0, "E MTAB 11083:2874F24 2 210715 D00404 0538 BCD91CANXX TCGACGTC TCTCTCCG L007", "0:51 1:0", "A:184971832;C:160126524;G:154012023;T:197490098;N:48201", 51, 0, null, null, 184971832, 160126524, 154012023, 197490098, 48201, "ERX6698607", "ERS8070396", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.6906, null, 0.15634, null, 0.75909, null, 0.51346, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10241, "ERR7131165", "ERX6698606", "ERS8070395", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F8 mCherry", "SAMEA10418611", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418611|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F8 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 8|organism part:olfactory bulb|sample name:E MTAB 11083:F8 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F8 mCherry s", "F8 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F23-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-CGTCTAAT_L006_R1_001.fastq.gz", "fastq", 667760646.0, 13093346.0, "E MTAB 11083:2874F23 1 210715 D00404 0538 BCD91CANXX TCGACGTC CGTCTAAT L006", "0:51 1:0", "A:179948739;C:150541918;G:145038845;T:192184092;N:47052", 51, 0, null, null, 179948739, 150541918, 145038845, 192184092, 47052, "ERX6698606", "ERS8070395", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.71661, null, 0.19774, null, 0.74576, null, 0.52117, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10242, "ERR7131166", "ERX6698606", "ERS8070395", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F8 mCherry", "SAMEA10418611", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418611|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F8 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 8|organism part:olfactory bulb|sample name:E MTAB 11083:F8 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F8 mCherry s", "F8 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F23-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-CGTCTAAT_L007_R1_001.fastq.gz", "fastq", 670970484.0, 13156284.0, "E MTAB 11083:2874F23 2 210715 D00404 0538 BCD91CANXX TCGACGTC CGTCTAAT L007", "0:51 1:0", "A:180906557;C:151329492;G:145816347;T:192872804;N:45284", 51, 0, null, null, 180906557, 151329492, 145816347, 192872804, 45284, "ERX6698606", "ERS8070395", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.71682, null, 0.19902, null, 0.74517, null, 0.52618, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10243, "ERR7131163", "ERX6698605", "ERS8070394", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F7 Nega", "SAMEA10418610", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418610|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F7 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 7|organism part:olfactory bulb|sample name:E MTAB 11083:F7 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F7 Nega s", "F7 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F19-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-GTAAGGAG_L006_R1_001.fastq.gz", "fastq", 652205238.0, 12788338.0, "E MTAB 11083:2874F19 1 210715 D00404 0538 BCD91CANXX TCGACGTC GTAAGGAG L006", "0:51 1:0", "A:173730405;C:149044598;G:145436777;T:183946928;N:46530", 51, 0, null, null, 173730405, 149044598, 145436777, 183946928, 46530, "ERX6698605", "ERS8070394", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.80595, null, 0.17309, null, 0.71003, null, 0.53696, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10244, "ERR7131164", "ERX6698605", "ERS8070394", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F7 Nega", "SAMEA10418610", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418610|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F7 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 7|organism part:olfactory bulb|sample name:E MTAB 11083:F7 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F7 Nega s", "F7 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F19-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-GTAAGGAG_L007_R1_001.fastq.gz", "fastq", 655593423.0, 12854773.0, "E MTAB 11083:2874F19 2 210715 D00404 0538 BCD91CANXX TCGACGTC GTAAGGAG L007", "0:51 1:0", "A:174715119;C:149844974;G:146250446;T:184737535;N:45349", 51, 0, null, null, 174715119, 149844974, 146250446, 184737535, 45349, "ERX6698605", "ERS8070394", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.80585, null, 0.17497, null, 0.71078, null, 0.53767, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10245, "ERR7131161", "ERX6698604", "ERS8070393", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F7 mCherry GFP", "SAMEA10418609", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418609|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F7 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 7|organism part:olfactory bulb|sample name:E MTAB 11083:F7 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F7 mCherry GFP s", "F7 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F21-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-AAGGAGTA_L006_R1_001.fastq.gz", "fastq", 661067151.0, 12962101.0, "E MTAB 11083:2874F21 1 210715 D00404 0538 BCD91CANXX TCGACGTC AAGGAGTA L006", "0:51 1:0", "A:168281419;C:157701209;G:153487197;T:181550252;N:47074", 51, 0, null, null, 168281419, 157701209, 153487197, 181550252, 47074, "ERX6698604", "ERS8070393", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.39074, null, 0.11592, null, 0.82615, null, 0.5252, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10246, "ERR7131162", "ERX6698604", "ERS8070393", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F7 mCherry GFP", "SAMEA10418609", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418609|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F7 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 7|organism part:olfactory bulb|sample name:E MTAB 11083:F7 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F7 mCherry GFP s", "F7 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F21-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-AAGGAGTA_L007_R1_001.fastq.gz", "fastq", 665709018.0, 13053118.0, "E MTAB 11083:2874F21 2 210715 D00404 0538 BCD91CANXX TCGACGTC AAGGAGTA L007", "0:51 1:0", "A:169539998;C:158884603;G:154624803;T:182614264;N:45350", 51, 0, null, null, 169539998, 158884603, 154624803, 182614264, 45350, "ERX6698604", "ERS8070393", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.38966, null, 0.1152, null, 0.8258, null, 0.53305, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10247, "ERR7131159", "ERX6698603", "ERS8070392", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F7 mCherry", "SAMEA10418608", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418608|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F7 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 7|organism part:olfactory bulb|sample name:E MTAB 11083:F7 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F7 mCherry s", "F7 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F20-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-ACTGCATA_L006_R1_001.fastq.gz", "fastq", 657813402.0, 12898302.0, "E MTAB 11083:2874F20 1 210715 D00404 0538 BCD91CANXX TCGACGTC ACTGCATA L006", "0:51 1:0", "A:175873489;C:149476129;G:143987770;T:188429588;N:46426", 51, 0, null, null, 175873489, 149476129, 143987770, 188429588, 46426, "ERX6698603", "ERS8070392", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.70507, null, 0.2048, null, 0.75923, null, 0.52828, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10248, "ERR7131160", "ERX6698603", "ERS8070392", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F7 mCherry", "SAMEA10418608", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418608|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F7 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 7|organism part:olfactory bulb|sample name:E MTAB 11083:F7 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F7 mCherry s", "F7 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F20-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-ACTGCATA_L007_R1_001.fastq.gz", "fastq", 660303426.0, 12947126.0, "E MTAB 11083:2874F20 2 210715 D00404 0538 BCD91CANXX TCGACGTC ACTGCATA L007", "0:51 1:0", "A:176607119;C:150065781;G:144613110;T:188972809;N:44607", 51, 0, null, null, 176607119, 150065781, 144613110, 188972809, 44607, "ERX6698603", "ERS8070392", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.70705, null, 0.20314, null, 0.75852, null, 0.52949, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10249, "ERR7131157", "ERX6698602", "ERS8070391", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F6 Nega", "SAMEA10418607", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418607|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F6 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 6|organism part:olfactory bulb|sample name:E MTAB 11083:F6 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F6 Nega s", "F6 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F16-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TCTCTCCG_L006_R1_001.fastq.gz", "fastq", 669627450.0, 13129950.0, "E MTAB 11083:2874F16 1 210715 D00404 0538 BCD91CANXX TGCAGCTA TCTCTCCG L006", "0:51 1:0", "A:177483937;C:154097051;G:148063012;T:189935690;N:47760", 51, 0, null, null, 177483937, 154097051, 148063012, 189935690, 47760, "ERX6698602", "ERS8070391", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.77183, null, 0.16001, null, 0.71467, null, 0.53352, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10250, "ERR7131158", "ERX6698602", "ERS8070391", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F6 Nega", "SAMEA10418607", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418607|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F6 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 6|organism part:olfactory bulb|sample name:E MTAB 11083:F6 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F6 Nega s", "F6 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F16-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TCTCTCCG_L007_R1_001.fastq.gz", "fastq", 671615073.0, 13168923.0, "E MTAB 11083:2874F16 2 210715 D00404 0538 BCD91CANXX TGCAGCTA TCTCTCCG L007", "0:51 1:0", "A:178109157;C:154619024;G:148595207;T:190246469;N:45216", 51, 0, null, null, 178109157, 154619024, 148595207, 190246469, 45216, "ERX6698602", "ERS8070391", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.77284, null, 0.15963, null, 0.71569, null, 0.53038, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10251, "ERR7131155", "ERX6698601", "ERS8070390", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F6 mCherry GFP", "SAMEA10418606", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418606|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F6 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 6|organism part:olfactory bulb|sample name:E MTAB 11083:F6 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F6 mCherry GFP s", "F6 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F18-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-TATCCTCT_L006_R1_001.fastq.gz", "fastq", 667663542.0, 13091442.0, "E MTAB 11083:2874F18 1 210715 D00404 0538 BCD91CANXX TCGACGTC TATCCTCT L006", "0:51 1:0", "A:177646483;C:152747528;G:146388226;T:190833951;N:47354", 51, 0, null, null, 177646483, 152747528, 146388226, 190833951, 47354, "ERX6698601", "ERS8070390", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.67964, null, 0.18123, null, 0.77193, null, 0.53313, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10252, "ERR7131156", "ERX6698601", "ERS8070390", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F6 mCherry GFP", "SAMEA10418606", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418606|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F6 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 6|organism part:olfactory bulb|sample name:E MTAB 11083:F6 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F6 mCherry GFP s", "F6 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F18-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-TATCCTCT_L007_R1_001.fastq.gz", "fastq", 670170141.0, 13140591.0, "E MTAB 11083:2874F18 2 210715 D00404 0538 BCD91CANXX TCGACGTC TATCCTCT L007", "0:51 1:0", "A:178425395;C:153363855;G:147033779;T:191300976;N:46136", 51, 0, null, null, 178425395, 153363855, 147033779, 191300976, 46136, "ERX6698601", "ERS8070390", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.67922, null, 0.18101, null, 0.77141, null, 0.53601, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10253, "ERR7131153", "ERX6698600", "ERS8070389", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F6 mCherry", "SAMEA10418605", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418605|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F6 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 6|organism part:olfactory bulb|sample name:E MTAB 11083:F6 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F6 mCherry s", "F6 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F17-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTCTCTAT_L006_R1_001.fastq.gz", "fastq", 677617008.0, 13286608.0, "E MTAB 11083:2874F17 1 210715 D00404 0538 BCD91CANXX TCGACGTC CTCTCTAT L006", "0:51 1:0", "A:181785899;C:152797687;G:147070676;T:195914808;N:47938", 51, 0, null, null, 181785899, 152797687, 147070676, 195914808, 47938, "ERX6698600", "ERS8070389", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.68298, null, 0.1953, null, 0.76292, null, 0.5395, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10254, "ERR7131154", "ERX6698600", "ERS8070389", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F6 mCherry", "SAMEA10418605", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418605|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F6 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 6|organism part:olfactory bulb|sample name:E MTAB 11083:F6 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F6 mCherry s", "F6 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F17-2_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTCTCTAT_L007_R1_001.fastq.gz", "fastq", 679922973.0, 13331823.0, "E MTAB 11083:2874F17 2 210715 D00404 0538 BCD91CANXX TCGACGTC CTCTCTAT L007", "0:51 1:0", "A:182567819;C:153380607;G:147589890;T:196337722;N:46935", 51, 0, null, null, 182567819, 153380607, 147589890, 196337722, 46935, "ERX6698600", "ERS8070389", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.68391, null, 0.19726, null, 0.76299, null, 0.54099, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10255, "ERR7131151", "ERX6698599", "ERS8070388", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F5 Nega", "SAMEA10418604", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418604|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F5 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 5|organism part:olfactory bulb|sample name:E MTAB 11083:F5 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F5 Nega s", "F5 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F13-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-AAGGAGTA_L006_R1_001.fastq.gz", "fastq", 620316315.0, 12163065.0, "E MTAB 11083:2874F13 1 210715 D00404 0538 BCD91CANXX TGCAGCTA AAGGAGTA L006", "0:51 1:0", "A:165967355;C:141072216;G:136931219;T:176301963;N:43562", 51, 0, null, null, 165967355, 141072216, 136931219, 176301963, 43562, "ERX6698599", "ERS8070388", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.78924, null, 0.17457, null, 0.71934, null, 0.53563, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10256, "ERR7131152", "ERX6698599", "ERS8070388", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F5 Nega", "SAMEA10418604", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418604|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F5 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 5|organism part:olfactory bulb|sample name:E MTAB 11083:F5 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F5 Nega s", "F5 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F13-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-AAGGAGTA_L007_R1_001.fastq.gz", "fastq", 623905338.0, 12233438.0, "E MTAB 11083:2874F13 2 210715 D00404 0538 BCD91CANXX TGCAGCTA AAGGAGTA L007", "0:51 1:0", "A:166996253;C:141937637;G:137825206;T:177103504;N:42738", 51, 0, null, null, 166996253, 141937637, 137825206, 177103504, 42738, "ERX6698599", "ERS8070388", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.78975, null, 0.17387, null, 0.72153, null, 0.54149, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10257, "ERR7131149", "ERX6698598", "ERS8070387", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F5 mCherry GFP", "SAMEA10418603", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418603|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F5 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 5|organism part:olfactory bulb|sample name:E MTAB 11083:F5 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F5 mCherry GFP s", "F5 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F15-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CGTCTAAT_L006_R1_001.fastq.gz", "fastq", 670154841.0, 13140291.0, "E MTAB 11083:2874F15 1 210715 D00404 0538 BCD91CANXX TGCAGCTA CGTCTAAT L006", "0:51 1:0", "A:182457480;C:149175456;G:144548173;T:193927470;N:46262", 51, 0, null, null, 182457480, 149175456, 144548173, 193927470, 46262, "ERX6698598", "ERS8070387", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.71875, null, 0.18671, null, 0.76047, null, 0.52398, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10258, "ERR7131150", "ERX6698598", "ERS8070387", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F5 mCherry GFP", "SAMEA10418603", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418603|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F5 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 5|organism part:olfactory bulb|sample name:E MTAB 11083:F5 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F5 mCherry GFP s", "F5 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F15-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CGTCTAAT_L007_R1_001.fastq.gz", "fastq", 674202048.0, 13219648.0, "E MTAB 11083:2874F15 2 210715 D00404 0538 BCD91CANXX TGCAGCTA CGTCTAAT L007", "0:51 1:0", "A:183639511;C:150168226;G:145502071;T:194847755;N:44485", 51, 0, null, null, 183639511, 150168226, 145502071, 194847755, 44485, "ERX6698598", "ERS8070387", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.72111, null, 0.18813, null, 0.76378, null, 0.5258, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10259, "ERR7131147", "ERX6698597", "ERS8070386", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F5 mCherry", "SAMEA10418602", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418602|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F5 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 5|organism part:olfactory bulb|sample name:E MTAB 11083:F5 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F5 mCherry s", "F5 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F14-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTAAGCCT_L006_R1_001.fastq.gz", "fastq", 615458259.0, 12067809.0, "E MTAB 11083:2874F14 1 210715 D00404 0538 BCD91CANXX TGCAGCTA CTAAGCCT L006", "0:51 1:0", "A:165108582;C:139178883;G:134070672;T:177059757;N:40365", 51, 0, null, null, 165108582, 139178883, 134070672, 177059757, 40365, "ERX6698597", "ERS8070386", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.69017, null, 0.1977, null, 0.77193, null, 0.53352, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10260, "ERR7131148", "ERX6698597", "ERS8070386", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F5 mCherry", "SAMEA10418602", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418602|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F5 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 5|organism part:olfactory bulb|sample name:E MTAB 11083:F5 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F5 mCherry s", "F5 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F14-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTAAGCCT_L007_R1_001.fastq.gz", "fastq", 619061613.0, 12138463.0, "E MTAB 11083:2874F14 2 210715 D00404 0538 BCD91CANXX TGCAGCTA CTAAGCCT L007", "0:51 1:0", "A:166167516;C:140058774;G:134972850;T:177822733;N:39740", 51, 0, null, null, 166167516, 140058774, 134972850, 177822733, 39740, "ERX6698597", "ERS8070386", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.69118, null, 0.20019, null, 0.7707, null, 0.52174, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10261, "ERR7131145", "ERX6698596", "ERS8070385", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F4 Nega", "SAMEA10418601", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418601|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F4 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 4|organism part:olfactory bulb|sample name:E MTAB 11083:F4 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F4 Nega s", "F4 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F10-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TATCCTCT_L006_R1_001.fastq.gz", "fastq", 652536687.0, 12794837.0, "E MTAB 11083:2874F10 1 210715 D00404 0538 BCD91CANXX TGCAGCTA TATCCTCT L006", "0:51 1:0", "A:178033231;C:144661707;G:139876661;T:189921085;N:44003", 51, 0, null, null, 178033231, 144661707, 139876661, 189921085, 44003, "ERX6698596", "ERS8070385", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.76201, null, 0.2508, null, 0.71299, null, 0.53379, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10262, "ERR7131146", "ERX6698596", "ERS8070385", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F4 Nega", "SAMEA10418601", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418601|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F4 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 4|organism part:olfactory bulb|sample name:E MTAB 11083:F4 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F4 Nega s", "F4 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F10-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-TATCCTCT_L007_R1_001.fastq.gz", "fastq", 655278957.0, 12848607.0, "E MTAB 11083:2874F10 2 210715 D00404 0538 BCD91CANXX TGCAGCTA TATCCTCT L007", "0:51 1:0", "A:178938002;C:145332613;G:140527756;T:190437189;N:43397", 51, 0, null, null, 178938002, 145332613, 140527756, 190437189, 43397, "ERX6698596", "ERS8070385", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.76188, null, 0.25356, null, 0.71344, null, 0.53081, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10263, "ERR7131143", "ERX6698595", "ERS8070384", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F4 mCherry GFP", "SAMEA10418600", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418600|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F4 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 4|organism part:olfactory bulb|sample name:E MTAB 11083:F4 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F4 mCherry GFP s", "F4 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F12-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-ACTGCATA_L006_R1_001.fastq.gz", "fastq", 297921855.0, 5841605.0, "E MTAB 11083:2874F12 1 210715 D00404 0538 BCD91CANXX TGCAGCTA ACTGCATA L006", "0:51 1:0", "A:82400724;C:65517496;G:64603058;T:85384480;N:16097", 51, 0, null, null, 82400724, 65517496, 64603058, 85384480, 16097, "ERX6698595", "ERS8070384", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.72496, null, 0.20794, null, 0.81223, null, 0.52529, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10264, "ERR7131144", "ERX6698595", "ERS8070384", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F4 mCherry GFP", "SAMEA10418600", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418600|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F4 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 4|organism part:olfactory bulb|sample name:E MTAB 11083:F4 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F4 mCherry GFP s", "F4 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F12-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-ACTGCATA_L007_R1_001.fastq.gz", "fastq", 309412971.0, 6066921.0, "E MTAB 11083:2874F12 2 210715 D00404 0538 BCD91CANXX TGCAGCTA ACTGCATA L007", "0:51 1:0", "A:85531271;C:68164437;G:67129209;T:88573210;N:14844", 51, 0, null, null, 85531271, 68164437, 67129209, 88573210, 14844, "ERX6698595", "ERS8070384", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.7245, null, 0.20724, null, 0.80468, null, 0.52791, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10265, "ERR7131141", "ERX6698594", "ERS8070383", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F4 mCherry", "SAMEA10418599", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418599|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F4 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 4|organism part:olfactory bulb|sample name:E MTAB 11083:F4 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F4 mCherry s", "F4 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F11-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-GTAAGGAG_L006_R1_001.fastq.gz", "fastq", 672319791.0, 13182741.0, "E MTAB 11083:2874F11 1 210715 D00404 0538 BCD91CANXX TGCAGCTA GTAAGGAG L006", "0:51 1:0", "A:181508034;C:150928549;G:146124085;T:193711358;N:47765", 51, 0, null, null, 181508034, 150928549, 146124085, 193711358, 47765, "ERX6698594", "ERS8070383", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.71726, null, 0.19842, null, 0.74986, null, 0.53363, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10266, "ERR7131142", "ERX6698594", "ERS8070383", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F4 mCherry", "SAMEA10418599", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418599|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F4 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 4|organism part:olfactory bulb|sample name:E MTAB 11083:F4 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F4 mCherry s", "F4 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F11-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-GTAAGGAG_L007_R1_001.fastq.gz", "fastq", 675486075.0, 13244825.0, "E MTAB 11083:2874F11 2 210715 D00404 0538 BCD91CANXX TGCAGCTA GTAAGGAG L007", "0:51 1:0", "A:182462261;C:151688554;G:146902713;T:194385945;N:46602", 51, 0, null, null, 182462261, 151688554, 146902713, 194385945, 46602, "ERX6698594", "ERS8070383", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.71745, null, 0.19727, null, 0.74805, null, 0.53092, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10267, "ERR7131139", "ERX6698593", "ERS8070382", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F3 Nega", "SAMEA10418598", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418598|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F3 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 3|organism part:olfactory bulb|sample name:E MTAB 11083:F3 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F3 Nega s", "F3 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F7-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-CGTCTAAT_L006_R1_001.fastq.gz", "fastq", 630093627.0, 12354777.0, "E MTAB 11083:2874F7 1 210715 D00404 0538 BCD91CANXX CGATCAGT CGTCTAAT L006", "0:51 1:0", "A:165132739;C:146179836;G:142796880;T:175940613;N:43559", 51, 0, null, null, 165132739, 146179836, 142796880, 175940613, 43559, "ERX6698593", "ERS8070382", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.81672, null, 0.15219, null, 0.71277, null, 0.52461, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10268, "ERR7131140", "ERX6698593", "ERS8070382", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F3 Nega", "SAMEA10418598", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418598|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F3 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 3|organism part:olfactory bulb|sample name:E MTAB 11083:F3 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F3 Nega s", "F3 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F7-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-CGTCTAAT_L007_R1_001.fastq.gz", "fastq", 632305242.0, 12398142.0, "E MTAB 11083:2874F7 2 210715 D00404 0538 BCD91CANXX CGATCAGT CGTCTAAT L007", "0:51 1:0", "A:165832174;C:146751895;G:143384539;T:176293313;N:43321", 51, 0, null, null, 165832174, 146751895, 143384539, 176293313, 43321, "ERX6698593", "ERS8070382", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.81791, null, 0.15444, null, 0.7151, null, 0.52585, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10269, "ERR7131137", "ERX6698592", "ERS8070381", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F3 mCherry GFP", "SAMEA10418597", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418597|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F3 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 3|organism part:olfactory bulb|sample name:E MTAB 11083:F3 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F3 mCherry GFP s", "F3 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F9-1_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTCTCTAT_L006_R1_001.fastq.gz", "fastq", 660379620.0, 12948620.0, "E MTAB 11083:2874F9 1 210715 D00404 0538 BCD91CANXX TGCAGCTA CTCTCTAT L006", "0:51 1:0", "A:178482695;C:147417787;G:143797476;T:190635173;N:46489", 51, 0, null, null, 178482695, 147417787, 143797476, 190635173, 46489, "ERX6698592", "ERS8070381", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.65635, null, 0.17778, null, 0.76899, null, 0.52957, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10270, "ERR7131138", "ERX6698592", "ERS8070381", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F3 mCherry GFP", "SAMEA10418597", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418597|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F3 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 3|organism part:olfactory bulb|sample name:E MTAB 11083:F3 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F3 mCherry GFP s", "F3 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F9-2_210715_D00404_0538_BCD91CANXX_TGCAGCTA-CTCTCTAT_L007_R1_001.fastq.gz", "fastq", 662411307.0, 12988457.0, "E MTAB 11083:2874F9 2 210715 D00404 0538 BCD91CANXX TGCAGCTA CTCTCTAT L007", "0:51 1:0", "A:179158323;C:147942300;G:144319925;T:190945370;N:45389", 51, 0, null, null, 179158323, 147942300, 144319925, 190945370, 45389, "ERX6698592", "ERS8070381", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.65813, null, 0.17896, null, 0.77076, null, 0.52835, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10271, "ERR7131135", "ERX6698591", "ERS8070380", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F3 mCherry", "SAMEA10418596", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418596|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F3 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 3|organism part:olfactory bulb|sample name:E MTAB 11083:F3 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F3 mCherry s", "F3 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F8-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-TCTCTCCG_L006_R1_001.fastq.gz", "fastq", 698608353.0, 13698203.0, "E MTAB 11083:2874F8 1 210715 D00404 0538 BCD91CANXX CGATCAGT TCTCTCCG L006", "0:51 1:0", "A:188718612;C:156814081;G:151125083;T:201901570;N:49007", 51, 0, null, null, 188718612, 156814081, 151125083, 201901570, 49007, "ERX6698591", "ERS8070380", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.70185, null, 0.21547, null, 0.75588, null, 0.53853, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10272, "ERR7131136", "ERX6698591", "ERS8070380", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F3 mCherry", "SAMEA10418596", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418596|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F3 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 3|organism part:olfactory bulb|sample name:E MTAB 11083:F3 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F3 mCherry s", "F3 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F8-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-TCTCTCCG_L007_R1_001.fastq.gz", "fastq", 699869175.0, 13722925.0, "E MTAB 11083:2874F8 2 210715 D00404 0538 BCD91CANXX CGATCAGT TCTCTCCG L007", "0:51 1:0", "A:189192315;C:157176897;G:151498983;T:201952867;N:48113", 51, 0, null, null, 189192315, 157176897, 151498983, 201952867, 48113, "ERX6698591", "ERS8070380", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.70221, null, 0.21684, null, 0.75621, null, 0.53787, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10273, "ERR7131133", "ERX6698590", "ERS8070379", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F2 Nega", "SAMEA10418595", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418595|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F2 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 2|organism part:olfactory bulb|sample name:E MTAB 11083:F2 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F2 Nega s", "F2 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F4-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-ACTGCATA_L006_R1_001.fastq.gz", "fastq", 573812985.0, 11251235.0, "E MTAB 11083:2874F4 1 210715 D00404 0538 BCD91CANXX CGATCAGT ACTGCATA L006", "0:51 1:0", "A:150716404;C:132203167;G:129732968;T:161120057;N:40389", 51, 0, null, null, 150716404, 132203167, 129732968, 161120057, 40389, "ERX6698590", "ERS8070379", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.81899, null, 0.17302, null, 0.72281, null, 0.54315, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10274, "ERR7131134", "ERX6698590", "ERS8070379", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F2 Nega", "SAMEA10418595", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418595|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F2 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 2|organism part:olfactory bulb|sample name:E MTAB 11083:F2 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F2 Nega s", "F2 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F4-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-ACTGCATA_L007_R1_001.fastq.gz", "fastq", 576184587.0, 11297737.0, "E MTAB 11083:2874F4 2 210715 D00404 0538 BCD91CANXX CGATCAGT ACTGCATA L007", "0:51 1:0", "A:151387408;C:132788210;G:130392043;T:161577529;N:39397", 51, 0, null, null, 151387408, 132788210, 130392043, 161577529, 39397, "ERX6698590", "ERS8070379", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.81999, null, 0.17082, null, 0.72196, null, 0.54505, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10275, "ERR7131131", "ERX6698589", "ERS8070378", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F2 mCherry GFP", "SAMEA10418594", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418594|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F2 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 2|organism part:olfactory bulb|sample name:E MTAB 11083:F2 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F2 mCherry GFP s", "F2 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F6-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTAAGCCT_L006_R1_001.fastq.gz", "fastq", 654811032.0, 12839432.0, "E MTAB 11083:2874F6 1 210715 D00404 0538 BCD91CANXX CGATCAGT CTAAGCCT L006", "0:51 1:0", "A:177403486;C:146202733;G:142207545;T:188951373;N:45895", 51, 0, null, null, 177403486, 146202733, 142207545, 188951373, 45895, "ERX6698589", "ERS8070378", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.67854, null, 0.21407, null, 0.76104, null, 0.52713, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10276, "ERR7131132", "ERX6698589", "ERS8070378", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F2 mCherry GFP", "SAMEA10418594", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418594|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F2 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 2|organism part:olfactory bulb|sample name:E MTAB 11083:F2 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F2 mCherry GFP s", "F2 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F6-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTAAGCCT_L007_R1_001.fastq.gz", "fastq", 656911926.0, 12880626.0, "E MTAB 11083:2874F6 2 210715 D00404 0538 BCD91CANXX CGATCAGT CTAAGCCT L007", "0:51 1:0", "A:178119212;C:146730132;G:142725348;T:189293212;N:44022", 51, 0, null, null, 178119212, 146730132, 142725348, 189293212, 44022, "ERX6698589", "ERS8070378", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.68162, null, 0.21431, null, 0.761, null, 0.5071, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10277, "ERR7131129", "ERX6698588", "ERS8070377", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F2 mCherry", "SAMEA10418593", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418593|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F2 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 2|organism part:olfactory bulb|sample name:E MTAB 11083:F2 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F2 mCherry s", "F2 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F5-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-AAGGAGTA_L006_R1_001.fastq.gz", "fastq", 607851558.0, 11918658.0, "E MTAB 11083:2874F5 1 210715 D00404 0538 BCD91CANXX CGATCAGT AAGGAGTA L006", "0:51 1:0", "A:164814138;C:136071648;G:132945950;T:173976881;N:42941", 51, 0, null, null, 164814138, 136071648, 132945950, 173976881, 42941, "ERX6698588", "ERS8070377", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.78967, null, 0.18905, null, 0.73241, null, 0.52347, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10278, "ERR7131130", "ERX6698588", "ERS8070377", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F2 mCherry", "SAMEA10418593", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418593|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F2 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 2|organism part:olfactory bulb|sample name:E MTAB 11083:F2 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F2 mCherry s", "F2 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F5-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-AAGGAGTA_L007_R1_001.fastq.gz", "fastq", 610931805.0, 11979055.0, "E MTAB 11083:2874F5 2 210715 D00404 0538 BCD91CANXX CGATCAGT AAGGAGTA L007", "0:51 1:0", "A:165714775;C:136822925;G:133684294;T:174667814;N:41997", 51, 0, null, null, 165714775, 136822925, 133684294, 174667814, 41997, "ERX6698588", "ERS8070377", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.78869, null, 0.18885, null, 0.73156, null, 0.51691, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10279, "ERR7131127", "ERX6698587", "ERS8070376", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F1 Nega", "SAMEA10418592", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418592|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F1 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 1|organism part:olfactory bulb|sample name:E MTAB 11083:F1 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F1 Nega s", "F1 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F1-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTCTCTAT_L006_R1_001.fastq.gz", "fastq", 619561872.0, 12148272.0, "E MTAB 11083:2874F1 1 210715 D00404 0538 BCD91CANXX CGATCAGT CTCTCTAT L006", "0:51 1:0", "A:164385545;C:141746313;G:138163219;T:175223323;N:43472", 51, 0, null, null, 164385545, 141746313, 138163219, 175223323, 43472, "ERX6698587", "ERS8070376", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.80258, null, 0.17703, null, 0.72614, null, 0.53483, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10280, "ERR7131128", "ERX6698587", "ERS8070376", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F1 Nega", "SAMEA10418592", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418592|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F1 Nega|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry /GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 1|organism part:olfactory bulb|sample name:E MTAB 11083:F1 Nega|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F1 Nega s", "F1 Nega s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry /GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F1-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-CTCTCTAT_L007_R1_001.fastq.gz", "fastq", 621481971.0, 12185921.0, "E MTAB 11083:2874F1 2 210715 D00404 0538 BCD91CANXX CGATCAGT CTCTCTAT L007", "0:51 1:0", "A:165030774;C:142231469;G:138651078;T:175527080;N:41570", 51, 0, null, null, 165030774, 142231469, 138651078, 175527080, 41570, "ERX6698587", "ERS8070376", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.80248, null, 0.17699, null, 0.726, null, 0.53711, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10281, "ERR7131125", "ERX6698586", "ERS8070375", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F1 mCherry GFP", "SAMEA10418591", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418591|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F1 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 1|organism part:olfactory bulb|sample name:E MTAB 11083:F1 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F1 mCherry GFP s", "F1 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F3-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-GTAAGGAG_L006_R1_001.fastq.gz", "fastq", 651189369.0, 12768419.0, "E MTAB 11083:2874F3 1 210715 D00404 0538 BCD91CANXX CGATCAGT GTAAGGAG L006", "0:51 1:0", "A:176398415;C:145659111;G:142137610;T:186948280;N:45953", 51, 0, null, null, 176398415, 145659111, 142137610, 186948280, 45953, "ERX6698586", "ERS8070375", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.69561, null, 0.18489, null, 0.75345, null, 0.52316, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10282, "ERR7131126", "ERX6698586", "ERS8070375", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F1 mCherry GFP", "SAMEA10418591", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418591|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F1 mCherry GFP|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP+|genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 1|organism part:olfactory bulb|sample name:E MTAB 11083:F1 mCherry GFP|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F1 mCherry GFP s", "F1 mCherry GFP s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP+", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F3-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-GTAAGGAG_L007_R1_001.fastq.gz", "fastq", 653398944.0, 12811744.0, "E MTAB 11083:2874F3 2 210715 D00404 0538 BCD91CANXX CGATCAGT GTAAGGAG L007", "0:51 1:0", "A:177139734;C:146171766;G:142707146;T:187335475;N:44823", 51, 0, null, null, 177139734, 146171766, 142707146, 187335475, 44823, "ERX6698586", "ERS8070375", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.69496, null, 0.18414, null, 0.75375, null, 0.52317, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10283, "ERR7131123", "ERX6698585", "ERS8070374", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F1 mCherry", "SAMEA10418590", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418590|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F1 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 1|organism part:olfactory bulb|sample name:E MTAB 11083:F1 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F1 mCherry s", "F1 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F2-1_210715_D00404_0538_BCD91CANXX_CGATCAGT-TATCCTCT_L006_R1_001.fastq.gz", "fastq", 613574319.0, 12030869.0, "E MTAB 11083:2874F2 1 210715 D00404 0538 BCD91CANXX CGATCAGT TATCCTCT L006", "0:51 1:0", "A:164891629;C:138401759;G:135818073;T:174419828;N:43030", 51, 0, null, null, 164891629, 138401759, 135818073, 174419828, 43030, "ERX6698585", "ERS8070374", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.79499, null, 0.21674, null, 0.73359, null, 0.52207, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [10284, "ERR7131124", "ERX6698585", "ERS8070374", "ERP132560", "PRJEB48218", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E-MTAB-11083", "Transcriptome Analysis", "To investigate the effects of rabies infection on neuronal gene expression  we compared gene profiles of rabies infected and non infected GABAergic neurons in the Zebrafish olfactory bulb.", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", null, "Protocols: EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "F1 mCherry", "SAMEA10418590", "Friedrich Miescher Institute for Biomedical Research", "ENA first public:2021 12 01|ENA last update:2021 12 01|External Id:SAMEA10418590|INSDC center alias:Friedrich Miescher Institute for Biomedical Research|INSDC center name:Friedrich Miescher Institute for Biomedical Research|INSDC first public:2021 12 01T00:23:59Z|INSDC last update:2021 12 01T00:23:59Z|INSDC status:public|Submitter Id:E MTAB 11083:F1 mCherry|age:9|broker name:ArrayExpress|cell type:GABAergic neuron|common name:zebrafish|developmental stage:adult|fraction:mCherry+/GFP |genotype:Tg[gad1b:Gal4  UAS:TVA mCherry]|individual:pool 1|organism part:olfactory bulb|sample name:E MTAB 11083:F1 mCherry|sex:mixed|stimulus:injected with EnvA RV GFP|strain:Ab x Tu x TL x WIK", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "E MTAB 11083:F1 mCherry s", "F1 mCherry s", "Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "EnvA RV GFP was injected to olfactory bulb in Tg[gad1b:Gal4  UAS:TVA mCherry] fish. Fish were kept in the standard fish system at 36 degree for 3 4 days. postwards  olfactory bulbs were extracted from 3 5 fish and the samples were pooled. post standard dissociation processes  cells were sorted by their fluorescent markers using LSRII. Batch 1 pool 1 to 3 was done 7 days before batch 2 pool 4 to 8. RNA was purified using single cell RNA purification Kit Norgen  cat. 51800 mRNA seq libraries were generated using the SmartSeq2 approach Picelli et al  Nature protocol 2014  with the following modifications: For cDNA pre amplification  up to 10ng of RNA was used as input typically 1 3ng  and Reverse Transcription was performed using Superscript IV Thermo Fisher Scientific   50C for 10min  80C for 10min. Amplified cDNA 1ng were converted to indexed sequencing libraries by tagmentation  using in house purified Tn5 Picelli et al  Genome Research 2014 and Illumina Nextera primers.", "Experimental Factor: fraction:mCherry+/GFP ", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP132560", "Illumina HiSeq 2500 sequencing; Effect of rabies virus infection on gene expression in GABAergic neurons in the Zebrafish olfactory bulb", "ENA FIRST PUBLIC:2022 07 07|ENA LAST UPDATE:2022 07 07", "2874F2-2_210715_D00404_0538_BCD91CANXX_CGATCAGT-TATCCTCT_L007_R1_001.fastq.gz", "fastq", 615666798.0, 12071898.0, "E MTAB 11083:2874F2 2 210715 D00404 0538 BCD91CANXX CGATCAGT TATCCTCT L007", "0:51 1:0", "A:165536502;C:138952758;G:136375193;T:174760659;N:41686", 51, 0, null, null, 165536502, 138952758, 136375193, 174760659, 41686, "ERX6698585", "ERS8070374", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.7941, null, 0.21645, null, 0.73494, null, 0.50761, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2021-12-01", "Adult", "Adult", "Brain", "Nervous System"], [29933, "SRR27592958", "SRX23261722", "SRS20163687", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep15", "GSM8020230", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep15", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b homozygous", "GSM8020230", "GSM8020230: arid1b  adult  rep15; Danio rerio; RNA Seq", "GSM8020230 r1", "GSM8020230", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-hom_A8_S20_R1_001.fastq.gz", "fastq", 4265635010.0, 42234010.0, "GSM8020230 r1", "0:101", "A:1152569190;C:1002056793;G:969860357;T:1141141715;N:6955", 101, null, null, null, 1152569190, 1002056793, 969860357, 1141141715, 6955, "SRX23261722", "SRS20163687", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29934, "SRR27592959", "SRX23261721", "SRS20163686", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep14", "GSM8020229", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep14", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b homozygous", "GSM8020229", "GSM8020229: arid1b  adult  rep14; Danio rerio; RNA Seq", "GSM8020229 r1", "GSM8020229", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-hom_A6_S18_R1_001.fastq.gz", "fastq", 1422969608.0, 14088808.0, "GSM8020229 r1", "0:101", "A:389767872;C:327820009;G:327097969;T:378282090;N:1668", 101, null, null, null, 389767872, 327820009, 327097969, 378282090, 1668, "SRX23261721", "SRS20163686", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29935, "SRR27592960", "SRX23261720", "SRS20163685", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep13", "GSM8020228", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b homozygous", "GSM8020228", "GSM8020228: arid1b  adult  rep13; Danio rerio; RNA Seq", "GSM8020228 r1", "GSM8020228", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-hom_A4_S16_R1_001.fastq.gz", "fastq", 4331217239.0, 42883339.0, "GSM8020228 r1", "0:101", "A:1169654932;C:1016829715;G:986390612;T:1158335000;N:6980", 101, null, null, null, 1169654932, 1016829715, 986390612, 1158335000, 6980, "SRX23261720", "SRS20163685", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29936, "SRR27592961", "SRX23261719", "SRS20163684", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep12", "GSM8020227", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b homozygous", "GSM8020227", "GSM8020227: arid1b  adult  rep12; Danio rerio; RNA Seq", "GSM8020227 r1", "GSM8020227", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-hom_A2_S14_R1_001.fastq.gz", "fastq", 820969107.0, 8128407.0, "GSM8020227 r1", "0:101", "A:229523100;C:185511734;G:179068656;T:226864374;N:1243", 101, null, null, null, 229523100, 185511734, 179068656, 226864374, 1243, "SRX23261719", "SRS20163684", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29937, "SRR27592962", "SRX23261718", "SRS20163683", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep11", "GSM8020226", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b heterozygous", "GSM8020226", "GSM8020226: arid1b  adult  rep11; Danio rerio; RNA Seq", "GSM8020226 r1", "GSM8020226", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-het_A7_S19_R1_001.fastq.gz", "fastq", 3609957150.0, 35742150.0, "GSM8020226 r1", "0:101", "A:997333826;C:818355353;G:803362992;T:990899286;N:5693", 101, null, null, null, 997333826, 818355353, 803362992, 990899286, 5693, "SRX23261718", "SRS20163683", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29938, "SRR27592963", "SRX23261717", "SRS20163682", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep10", "GSM8020225", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b heterozygous", "GSM8020225", "GSM8020225: arid1b  adult  rep10; Danio rerio; RNA Seq", "GSM8020225 r1", "GSM8020225", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-het_A5_S17_R1_001.fastq.gz", "fastq", 3177521913.0, 31460613.0, "GSM8020225 r1", "0:101", "A:869322737;C:728803554;G:719191487;T:860199264;N:4871", 101, null, null, null, 869322737, 728803554, 719191487, 860199264, 4871, "SRX23261717", "SRS20163682", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29939, "SRR27592964", "SRX23261716", "SRS20163681", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep9", "GSM8020224", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b heterozygous", "GSM8020224", "GSM8020224: arid1b  adult  rep9; Danio rerio; RNA Seq", "GSM8020224 r1", "GSM8020224", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-het_A3_S15_R1_001.fastq.gz", "fastq", 3681640688.0, 36451888.0, "GSM8020224 r1", "0:101", "A:972550652;C:881056608;G:858084187;T:969943492;N:5749", 101, null, null, null, 972550652, 881056608, 858084187, 969943492, 5749, "SRX23261716", "SRS20163681", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29940, "SRR27592965", "SRX23261715", "SRS20163679", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep8", "GSM8020223", null, "source name:single dissected adult brain  male|tissue:single dissected adult brain  male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  male", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  male|genotype:arid1b heterozygous", "GSM8020223", "GSM8020223: arid1b  adult  rep8; Danio rerio; RNA Seq", "GSM8020223 r1", "GSM8020223", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set2-het_A1_S13_R1_001.fastq.gz", "fastq", 2692714540.0, 26660540.0, "GSM8020223 r1", "0:101", "A:739519019;C:619307370;G:594887957;T:738995900;N:4294", 101, null, null, null, 739519019, 619307370, 594887957, 738995900, 4294, "SRX23261715", "SRS20163679", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29941, "SRR27592966", "SRX23261714", "SRS20163680", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep7", "GSM8020222", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b homozygous", "GSM8020222", "GSM8020222: arid1b  adult  rep7; Danio rerio; RNA Seq", "GSM8020222 r1", "GSM8020222", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-hom_8_S38_R1_001.fastq.gz", "fastq", 3385303153.0, 33517853.0, "GSM8020222 r1", "0:101", "A:922612734;C:831122592;G:725118400;T:906435529;N:13898", 101, null, null, null, 922612734, 831122592, 725118400, 906435529, 13898, "SRX23261714", "SRS20163680", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29942, "SRR27592967", "SRX23261713", "SRS20163678", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep6", "GSM8020221", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b homozygous", "GSM8020221", "GSM8020221: arid1b  adult  rep6; Danio rerio; RNA Seq", "GSM8020221 r1", "GSM8020221", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-hom_6_S36_R1_001.fastq.gz", "fastq", 4453651055.0, 44095555.0, "GSM8020221 r1", "0:101", "A:1190308155;C:1078598974;G:1012348343;T:1172377706;N:17877", 101, null, null, null, 1190308155, 1078598974, 1012348343, 1172377706, 17877, "SRX23261713", "SRS20163678", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29943, "SRR27592968", "SRX23261712", "SRS20163677", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep5", "GSM8020220", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b homozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b homozygous", "GSM8020220", "GSM8020220: arid1b  adult  rep5; Danio rerio; RNA Seq", "GSM8020220 r1", "GSM8020220", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-hom_5_S35_R1_001.fastq.gz", "fastq", 3607941998.0, 35722198.0, "GSM8020220 r1", "0:101", "A:986679637;C:834475298;G:801712371;T:985059988;N:14704", 101, null, null, null, 986679637, 834475298, 801712371, 985059988, 14704, "SRX23261712", "SRS20163677", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29944, "SRR27592969", "SRX23261711", "SRS20163675", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep4", "GSM8020219", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b heterozygous", "GSM8020219", "GSM8020219: arid1b  adult  rep4; Danio rerio; RNA Seq", "GSM8020219 r1", "GSM8020219", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-het_4_S34_R1_001.fastq.gz", "fastq", 3406563249.0, 33728349.0, "GSM8020219 r1", "0:101", "A:929693102;C:825436822;G:742465339;T:908956167;N:11819", 101, null, null, null, 929693102, 825436822, 742465339, 908956167, 11819, "SRX23261711", "SRS20163675", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29945, "SRR27592970", "SRX23261710", "SRS20163676", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep3", "GSM8020218", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b heterozygous", "GSM8020218", "GSM8020218: arid1b  adult  rep3; Danio rerio; RNA Seq", "GSM8020218 r1", "GSM8020218", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-het_3_S33_R1_001.fastq.gz", "fastq", 3437288459.0, 34032559.0, "GSM8020218 r1", "0:101", "A:936275875;C:807195445;G:746272516;T:947530775;N:13848", 101, null, null, null, 936275875, 807195445, 746272516, 947530775, 13848, "SRX23261710", "SRS20163676", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29946, "SRR27592971", "SRX23261709", "SRS20163674", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep2", "GSM8020217", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b heterozygous", "GSM8020217", "GSM8020217: arid1b  adult  rep2; Danio rerio; RNA Seq", "GSM8020217 r1", "GSM8020217", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-het_2_S32_R1_001.fastq.gz", "fastq", 3033976067.0, 30039367.0, "GSM8020217 r1", "0:101", "A:813028951;C:730788577;G:668973332;T:821173824;N:11383", 101, null, null, null, 813028951, 730788577, 668973332, 821173824, 11383, "SRX23261709", "SRS20163674", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [29971, "SRR27592996", "SRX23261684", "SRS20163649", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "arid1b  adult  rep1", "GSM8020216", null, "source name:single dissected adult brain  female|tissue:single dissected adult brain  female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing", "arid1b  adult  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "single dissected adult brain  female", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:single dissected adult brain  female|genotype:arid1b heterozygous", "GSM8020216", "GSM8020216: arid1b  adult  rep1; Danio rerio; RNA Seq", "GSM8020216 r1", "GSM8020216", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "arid1b-adult-set1-het_1_S31_R1_001.fastq.gz", "fastq", 2831462785.0, 28034285.0, "GSM8020216 r1", "0:101", "A:770779666;C:662406160;G:622932995;T:775332651;N:11313", 101, null, null, null, 770779666, 662406160, 622932995, 775332651, 11313, "SRX23261684", "SRS20163649", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Adult", "Adult", "Brain", "Nervous System"], [34554, "SRR32104359", "SRX27449951", "SRS23876473", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Negative CNC 3", "GSM8751784", null, "source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  |geo loc name:missing|collection date:missing", "17hpf Negative CNC 3", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "non neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  ", "GSM8751784", "GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq", "GSM8751784 r1", "GSM8751784", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz", "fastq", 6549316700.0, 65493167.0, "GSM8751784 r1", "0:100", "A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591", 100, null, null, null, 1904137226, 1372226751, 1395882591, 1876995541, 74591, "SRX27449951", "SRS23876473", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [34555, "SRR32104360", "SRX27449950", "SRS23876471", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Negative CNC 2", "GSM8751783", null, "source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  |geo loc name:missing|collection date:missing", "17hpf Negative CNC 2", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "non neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  ", "GSM8751783", "GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq", "GSM8751783 r1", "GSM8751783", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz", "fastq", 2595442300.0, 51908846.0, "GSM8751783 r1", "0:50", "A:735396784;C:561568693;G:572114011;T:726356371;N:6441", 50, null, null, null, 735396784, 561568693, 572114011, 726356371, 6441, "SRX27449950", "SRS23876471", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [34556, "SRR32104361", "SRX27449949", "SRS23876470", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Negative CNC 1", "GSM8751782", null, "source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  |geo loc name:missing|collection date:missing", "17hpf Negative CNC 1", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "non neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry  ", "GSM8751782", "GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq", "GSM8751782 r1", "GSM8751782", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz", "fastq", 2554400850.0, 51088017.0, "GSM8751782 r1", "0:50", "A:739730182;C:537827580;G:551508245;T:725296198;N:38645", 50, null, null, null, 739730182, 537827580, 551508245, 725296198, 38645, "SRX27449949", "SRS23876470", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [66168, "SRR15931293", "SRX12221404", "SRS10197471", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/+ 4dpf eNCC #1", "GSM5585062", null, "tissue:enteric Neural Crest Cells|genotype:chd8 +/+", "chd8+/+ 4dpf eNCC #1", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8 +/+", "GSM5585062", "GSM5585062: chd8+/+ 4dpf eNCC #1; Danio rerio; RNA Seq", "GSM5585062", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585062", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT1.fastq.gz", "fastq", 2075182700.0, 41503654.0, "GSM5585062 r1", "0:50", "A:596606751;C:434020268;G:443333228;T:601159724;N:62729", 50, null, null, null, 596606751, 434020268, 443333228, 601159724, 62729, "SRX12221404", "SRS10197471", "SRA1296090", "GEO", "IGBMC", 1, 0.8763, null, 0.23634, null, 0.7349, null, 0.56679, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66169, "SRR15931300", "SRX12221403", "SRS10197470", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/  4dpf eNCC #4", "GSM5585069", null, "tissue:enteric Neural Crest Cells|genotype:chd8+/ ", "chd8+/  4dpf eNCC #4", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8+/ ", "GSM5585069", "GSM5585069: chd8+/  4dpf eNCC #4; Danio rerio; RNA Seq", "GSM5585069", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585069", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT8.fastq.gz", "fastq", 2166642350.0, 43332847.0, "GSM5585069 r1", "0:50", "A:605269250;C:463067293;G:474978141;T:623262976;N:64690", 50, null, null, null, 605269250, 463067293, 474978141, 623262976, 64690, "SRX12221403", "SRS10197470", "SRA1296090", "GEO", "IGBMC", 1, 0.87709, null, 0.18108, null, 0.73091, null, 0.55465, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66170, "SRR15931299", "SRX12221402", "SRS10197468", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/  4dpf eNCC #3", "GSM5585068", null, "tissue:enteric Neural Crest Cells|genotype:chd8+/ ", "chd8+/  4dpf eNCC #3", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8+/ ", "GSM5585068", "GSM5585068: chd8+/  4dpf eNCC #3; Danio rerio; RNA Seq", "GSM5585068", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585068", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT7.fastq.gz", "fastq", 2044848000.0, 40896960.0, "GSM5585068 r1", "0:50", "A:570340694;C:448773695;G:458077948;T:567595155;N:60508", 50, null, null, null, 570340694, 448773695, 458077948, 567595155, 60508, "SRX12221402", "SRS10197468", "SRA1296090", "GEO", "IGBMC", 1, 0.89989, null, 0.13688, null, 0.74761, null, 0.51955, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66171, "SRR15931298", "SRX12221401", "SRS10197467", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/  4dpf eNCC #2", "GSM5585067", null, "tissue:enteric Neural Crest Cells|genotype:chd8+/ ", "chd8+/  4dpf eNCC #2", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8+/ ", "GSM5585067", "GSM5585067: chd8+/  4dpf eNCC #2; Danio rerio; RNA Seq", "GSM5585067", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT6.fastq.gz", "fastq", 2236566700.0, 44731334.0, "GSM5585067 r1", "0:50", "A:632520025;C:482922105;G:493836270;T:627225283;N:63017", 50, null, null, null, 632520025, 482922105, 493836270, 627225283, 63017, "SRX12221401", "SRS10197467", "SRA1296090", "GEO", "IGBMC", 1, 0.87472, null, 0.13005, null, 0.73214, null, 0.54467, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66172, "SRR15931297", "SRX12221400", "SRS10197469", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/  4dpf eNCC #1", "GSM5585066", null, "tissue:enteric Neural Crest Cells|genotype:chd8+/ ", "chd8+/  4dpf eNCC #1", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8+/ ", "GSM5585066", "GSM5585066: chd8+/  4dpf eNCC #1; Danio rerio; RNA Seq", "GSM5585066", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT5.fastq.gz", "fastq", 2445365700.0, 48907314.0, "GSM5585066 r1", "0:50", "A:652878336;C:569347668;G:578346047;T:644721788;N:71861", 50, null, null, null, 652878336, 569347668, 578346047, 644721788, 71861, "SRX12221400", "SRS10197469", "SRA1296090", "GEO", "IGBMC", 1, 0.91958, null, 0.08571, null, 0.72222, null, 0.51361, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66173, "SRR15931296", "SRX12221399", "SRS10197466", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/+ 4dpf eNCC #4", "GSM5585065", null, "tissue:enteric Neural Crest Cells|genotype:chd8 +/+", "chd8+/+ 4dpf eNCC #4", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8 +/+", "GSM5585065", "GSM5585065: chd8+/+ 4dpf eNCC #4; Danio rerio; RNA Seq", "GSM5585065", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT4.fastq.gz", "fastq", 2016451500.0, 40329030.0, "GSM5585065 r1", "0:50", "A:554611579;C:447165784;G:458213114;T:556400342;N:60681", 50, null, null, null, 554611579, 447165784, 458213114, 556400342, 60681, "SRX12221399", "SRS10197466", "SRA1296090", "GEO", "IGBMC", 1, 0.89742, null, 0.11584, null, 0.72127, null, 0.52068, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66174, "SRR15931295", "SRX12221398", "SRS10197465", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/+ 4dpf eNCC #3", "GSM5585064", null, "tissue:enteric Neural Crest Cells|genotype:chd8 +/+", "chd8+/+ 4dpf eNCC #3", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8 +/+", "GSM5585064", "GSM5585064: chd8+/+ 4dpf eNCC #3; Danio rerio; RNA Seq", "GSM5585064", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT3.fastq.gz", "fastq", 2081908800.0, 41638176.0, "GSM5585064 r1", "0:50", "A:583234858;C:447061909;G:457587573;T:593962758;N:61702", 50, null, null, null, 583234858, 447061909, 457587573, 593962758, 61702, "SRX12221398", "SRS10197465", "SRA1296090", "GEO", "IGBMC", 1, 0.88033, null, 0.16506, null, 0.75138, null, 0.50655, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [66175, "SRR15931294", "SRX12221397", "SRS10197464", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/+ 4dpf eNCC #2", "GSM5585063", null, "tissue:enteric Neural Crest Cells|genotype:chd8 +/+", "chd8+/+ 4dpf eNCC #2", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8 +/+", "GSM5585063", "GSM5585063: chd8+/+ 4dpf eNCC #2; Danio rerio; RNA Seq", "GSM5585063", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT2.fastq.gz", "fastq", 2151869900.0, 43037398.0, "GSM5585063 r1", "0:50", "A:581790111;C:491684308;G:500076074;T:578254560;N:64847", 50, null, null, null, 581790111, 491684308, 500076074, 578254560, 64847, "SRX12221397", "SRS10197464", "SRA1296090", "GEO", "IGBMC", 1, 0.915, null, 0.08656, null, 0.72537, null, 0.52001, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous System"], [75652, "SRR24758212", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A01.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 196502541.0, 3852991.0, "GSM7432137 r1", "0:51", "A:49165276;C:47981089;G:48399038;T:50940008;N:17130", 51, null, null, null, 49165276, 47981089, 48399038, 50940008, 17130, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.72705, null, 0.06867, null, 0.88552, null, 0.54207, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75653, "SRR24758213", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A10.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 57801819.0, 1133369.0, "GSM7432137 r10", "0:51", "A:15530697;C:12658068;G:12843873;T:16764026;N:5155", 51, null, null, null, 15530697, 12658068, 12843873, 16764026, 5155, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.63663, null, 0.42833, null, 0.92111, null, 0.57817, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75654, "SRR24758214", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A11.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 72272559.0, 1417109.0, "GSM7432137 r11", "0:51", "A:18233220;C:16632293;G:17042518;T:20358144;N:6384", 51, null, null, null, 18233220, 16632293, 17042518, 20358144, 6384, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.67945, null, 0.12353, null, 0.94095, null, 0.48607, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75655, "SRR24758215", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A12.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 187811019.0, 3682569.0, "GSM7432137 r12", "0:51", "A:49325726;C:43713702;G:44241940;T:50513058;N:16593", 51, null, null, null, 49325726, 43713702, 44241940, 50513058, 16593, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.84473, null, 0.12213, null, 0.90666, null, 0.56528, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75656, "SRR24758216", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B01.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 24050070.0, 471570.0, "GSM7432137 r13", "0:51", "A:5907474;C:6114990;G:5982982;T:6042494;N:2130", 51, null, null, null, 5907474, 6114990, 5982982, 6042494, 2130, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.47163, null, 0.30199, null, 0.93933, null, 0.53872, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75657, "SRR24758217", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B02.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 275774544.0, 5407344.0, "GSM7432137 r14", "0:51", "A:69654405;C:67726837;G:68298856;T:70070552;N:23894", 51, null, null, null, 69654405, 67726837, 68298856, 70070552, 23894, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.84442, null, 0.07023, null, 0.88923, null, 0.53422, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75658, "SRR24758218", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 226648335.0, 4444085.0, "GSM7432137 r15", "0:51", "A:57531232;C:54256013;G:54956617;T:59884654;N:19819", 51, null, null, null, 57531232, 54256013, 54956617, 59884654, 19819, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.80693, null, 0.10694, null, 0.9179, null, 0.52785, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75659, "SRR24758219", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B04.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 247590159.0, 4854709.0, "GSM7432137 r16", "0:51", "A:64151909;C:59176102;G:59606872;T:64633924;N:21352", 51, null, null, null, 64151909, 59176102, 59606872, 64633924, 21352, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.85951, null, 0.0727, null, 0.88598, null, 0.52101, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75660, "SRR24758220", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B05.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 236963799.0, 4646349.0, "GSM7432137 r17", "0:51", "A:61256843;C:56596118;G:57122766;T:61967590;N:20482", 51, null, null, null, 61256843, 56596118, 57122766, 61967590, 20482, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.86507, null, 0.0857, null, 0.89556, null, 0.38852, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75661, "SRR24758221", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B06.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 174345642.0, 3418542.0, "GSM7432137 r18", "0:51", "A:43218316;C:42711053;G:43771526;T:44629449;N:15298", 51, null, null, null, 43218316, 42711053, 43771526, 44629449, 15298, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.85865, null, 0.02991, null, 0.91167, null, 0.40975, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75662, "SRR24758222", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B07.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 310253298.0, 6083398.0, "GSM7432137 r19", "0:51", "A:79341090;C:74303124;G:75662036;T:80919848;N:27200", 51, null, null, null, 79341090, 74303124, 75662036, 80919848, 27200, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.87708, null, 0.0717, null, 0.89727, null, 0.46207, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75663, "SRR24758223", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A02.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 566253.0, 11103.0, "GSM7432137 r2", "0:51", "A:136988;C:128378;G:125521;T:175317;N:49", 51, null, null, null, 136988, 128378, 125521, 175317, 49, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.67766, null, 0.11307, null, 0.95172, null, 0.5382, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75664, "SRR24758224", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B08.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 346341.0, 6791.0, "GSM7432137 r20", "0:51", "A:84780;C:84123;G:83720;T:93689;N:29", 51, null, null, null, 84780, 84123, 83720, 93689, 29, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.63515, null, 0.09273, null, 0.96802, null, 0.52162, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75665, "SRR24758225", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B09.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 377961.0, 7411.0, "GSM7432137 r21", "0:51", "A:95293;C:90257;G:87563;T:104807;N:41", 51, null, null, null, 95293, 90257, 87563, 104807, 41, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.69105, null, 0.08086, null, 0.96455, null, 0.53115, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75666, "SRR24758226", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B10.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 2250936.0, 44136.0, "GSM7432137 r22", "0:51", "A:539924;C:650712;G:518629;T:541473;N:198", 51, null, null, null, 539924, 650712, 518629, 541473, 198, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.27445, null, 0.04803, null, 0.95276, null, 0.53885, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75667, "SRR24758227", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B11.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 207937659.0, 4077209.0, "GSM7432137 r23", "0:51", "A:52800304;C:49954044;G:50494891;T:54670231;N:18189", 51, null, null, null, 52800304, 49954044, 50494891, 54670231, 18189, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.83348, null, 0.06056, null, 0.87643, null, 0.52466, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75668, "SRR24758228", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_B12.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 116941317.0, 2292967.0, "GSM7432137 r24", "0:51", "A:31454818;C:25883611;G:26279868;T:33312749;N:10271", 51, null, null, null, 31454818, 25883611, 26279868, 33312749, 10271, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.76622, null, 0.21094, null, 0.92413, null, 0.55894, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75669, "SRR24758229", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C01.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 539172.0, 10572.0, "GSM7432137 r25", "0:51", "A:134771;C:127049;G:127559;T:149745;N:48", 51, null, null, null, 134771, 127049, 127559, 149745, 48, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.74289, null, 0.09475, null, 0.94769, null, 0.55262, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75670, "SRR24758230", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C02.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 249154176.0, 4885376.0, "GSM7432137 r26", "0:51", "A:62840979;C:61240493;G:61835852;T:63215177;N:21675", 51, null, null, null, 62840979, 61240493, 61835852, 63215177, 21675, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.89326, null, 0.07803, null, 0.84967, null, 0.51569, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75671, "SRR24758231", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 641019.0, 12569.0, "GSM7432137 r27", "0:51", "A:175739;C:156164;G:141289;T:167772;N:55", 51, null, null, null, 175739, 156164, 141289, 167772, 55, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.50169, null, 0.06287, null, 0.95611, null, 0.57318, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75672, "SRR24758232", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C04.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 223399839.0, 4380389.0, "GSM7432137 r28", "0:51", "A:58104465;C:53189406;G:53552668;T:58534071;N:19229", 51, null, null, null, 58104465, 53189406, 53552668, 58534071, 19229, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.84775, null, 0.07316, null, 0.89883, null, 0.53245, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75673, "SRR24758233", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C05.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 2148528.0, 42128.0, "GSM7432137 r29", "0:51", "A:456160;C:713081;G:433891;T:545183;N:213", 51, null, null, null, 456160, 713081, 433891, 545183, 213, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.31226, null, 0.04264, null, 0.94718, null, 0.54464, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75674, "SRR24758234", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 182987337.0, 3587987.0, "GSM7432137 r3", "0:51", "A:48471316;C:41287723;G:41835653;T:51376450;N:16195", 51, null, null, null, 48471316, 41287723, 41835653, 51376450, 16195, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.79625, null, 0.12945, null, 0.87042, null, 0.54466, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75675, "SRR24758235", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C06.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 277189131.0, 5435081.0, "GSM7432137 r30", "0:51", "A:72722594;C:65268944;G:65970657;T:73202676;N:24260", 51, null, null, null, 72722594, 65268944, 65970657, 73202676, 24260, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.85793, null, 0.09135, null, 0.89428, null, 0.53659, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75676, "SRR24758236", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C07.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 51855423.0, 1016773.0, "GSM7432137 r31", "0:51", "A:12581543;C:12652880;G:12719547;T:13896926;N:4527", 51, null, null, null, 12581543, 12652880, 12719547, 13896926, 4527, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.64717, null, 0.1549, null, 0.93042, null, 0.59143, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"], [75677, "SRR24758237", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_C08.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 196417422.0, 3851322.0, "GSM7432137 r32", "0:51", "A:49916233;C:47717459;G:48374054;T:50392337;N:17339", 51, null, null, null, 49916233, 47717459, 48374054, 50392337, 17339, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.75845, null, 0.10284, null, 0.91001, null, 0.55748, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 650, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", 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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 from run_metadata where \"experiment.library_layout\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "smartseq", "p2": "Brain"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=smartseq&tissue_curation=Brain", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 650, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=smartseq&tissue_curation=Brain&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": 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