{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"Oligo-dT\" and experiment.library_source = \"TRANSCRIPTOMIC\"", "rows": [[3759, "ERR1294279", "ERX1365625", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9", "vbu13", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu13_GCCAAT_L008_R1_001.fastq.gz", "fastq", 2376143675.0, 23526175.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9", "0:101", "A:655940769;C:534990399;G:527934646;T:655773043;N:1504818", 101, null, null, null, 655940769, 534990399, 527934646, 655773043, 1504818, "ERX1365625", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95443, null, 0.10666, null, 0.73176, null, 0.50978, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3760, "ERR1294278", "ERX1365624", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. 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To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5", "ve12", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve12_ATGTCA_L008_R1_001.fastq.gz", "fastq", 1446322222.0, 14320022.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5", "0:101", "A:400821160;C:324210104;G:320286425;T:400078485;N:926048", 101, null, null, null, 400821160, 324210104, 320286425, 400078485, 926048, "ERX1365621", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.92778, null, 0.09489, null, 0.73093, null, 0.48493, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3764, "ERR1294274", "ERX1365620", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. 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To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3", "wt3", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt3_AGTCAA_L008_R1_001.fastq.gz", "fastq", 2631687411.0, 26056311.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3", "0:101", "A:734843629;C:584316000;G:577487406;T:733356850;N:1683526", 101, null, null, null, 734843629, 584316000, 577487406, 733356850, 1683526, "ERX1365619", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95114, null, 0.1036, null, 0.72474, null, 0.48261, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3766, "ERR1294272", "ERX1365618", "ERS1067818", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. 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To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1", "wt1", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt1_CAGATC_L008_R1_001.fastq.gz", "fastq", 1701561241.0, 16847141.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1", "0:101", "A:505358711;C:348893979;G:343445186;T:502880170;N:983195", 101, null, null, null, 505358711, 348893979, 343445186, 502880170, 983195, "ERX1365617", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.94565, null, 0.13032, null, 0.73669, null, 0.50473, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [5879, "ERR1759701", "ERX1826022", "ERS1474296", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample2", "SAMEA27136168", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample2 s", "Sample2 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz", "fastq", 448234901.0, 6016977.0, "E MTAB 5323:Sample2", "0:74.50 1:0", "A:118923409;C:100586009;G:99987046;T:126071553;N:2666884", 74, 0, null, null, 118923409, 100586009, 99987046, 126071553, 2666884, "ERX1826022", "ERS1474296", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.88465, null, 0.27583, null, 0.75398, null, 0.55917, null, 75, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5880, "ERR1759702", "ERX1826022", "ERS1474296", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample2", "SAMEA27136168", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample2 s", "Sample2 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz", "fastq", 448116860.0, 6016977.0, "E MTAB 5323:Sample2 1", "0:0 1:74.48", "A:127811460;C:99875207;G:106561979;T:113792335;N:75879", 0, 74, null, null, 127811460, 99875207, 106561979, 113792335, 75879, "ERX1826022", "ERS1474296", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.91589, null, 0.2509, null, 0.79005, null, 0.54852, null, 75, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5881, "ERR1759699", "ERX1826021", "ERS1474295", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample1", "SAMEA27135418", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample1 s", "Sample1 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz", "fastq", 766363334.0, 10284347.0, "E MTAB 5323:Sample1", "0:74.52 1:0", "A:201960096;C:174999154;G:173403690;T:211341998;N:4658396", 74, 0, null, null, 201960096, 174999154, 173403690, 211341998, 4658396, "ERX1826021", "ERS1474295", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.86003, null, 0.20554, null, 0.76301, null, 0.55753, null, 74, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5882, "ERR1759700", "ERX1826021", "ERS1474295", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample1", "SAMEA27135418", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample1 s", "Sample1 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz", "fastq", 766251339.0, 10284347.0, "E MTAB 5323:Sample1 1", "0:0 1:74.51", "A:214234414;C:174215653;G:180382062;T:197361982;N:57228", 0, 74, null, null, 214234414, 174215653, 180382062, 197361982, 57228, "ERX1826021", "ERS1474295", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.87766, null, 0.21561, null, 0.77477, null, 0.53919, null, 73, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [9361, "ERR3011947", "ERX3014407", "ERS2994081", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Flutamide 2", "SAMEA5186582", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186582|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 2|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:Flutamide 2 s", "Flutamide 2 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:flutamide|Experimental Factor: dose:10", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_Flutamide_2_R1.fastq.gz", "fastq", 1754963940.0, 23552243.0, "E MTAB 7283:Flutamide 2", "0:74.51 1:0", "A:455444321;C:410713896;G:385640226;T:503155736;N:9761", 74, 0, null, null, 455444321, 410713896, 385640226, 503155736, 9761, "ERX3014407", "ERS2994081", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94351, null, 0.11595, null, 0.67483, null, 0.48762, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9362, "ERR3011946", "ERX3014406", "ERS2994080", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Flutamide 1", "SAMEA5186581", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186581|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 1|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:Flutamide 1 s", "Flutamide 1 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:flutamide|Experimental Factor: dose:10", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_Flutamide_1_R1.fastq.gz", "fastq", 1631102863.0, 21898245.0, "E MTAB 7283:Flutamide 1", "0:74.49 1:0", "A:424378341;C:380806325;G:358128992;T:467779945;N:9260", 74, 0, null, null, 424378341, 380806325, 358128992, 467779945, 9260, "ERX3014406", "ERS2994080", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94332, null, 0.11797, null, 0.67596, null, 0.48847, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9363, "ERR3011945", "ERX3014405", "ERS2994079", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "DMSO 2", "SAMEA5186580", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186580|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 2|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:DMSO 2 s", "DMSO 2 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. 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Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "DMSO 1", "SAMEA5186579", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186579|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 1|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:DMSO 1 s", "DMSO 1 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. 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UPDATE:2022 07 05", null, "WT 6h rep1", "WT 6h rep1", "JD AC29 PDBN024889", null, "ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, null, null, null, null, "PromethION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "PromethION", null, "ERP122761", "PromethION sequencing", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", "JD-AC29_PDBN024889.tar.gz", "nanopore", 1900324756.0, 2013035.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2", "0:944.01", "A:549431032;C:411510218;G:422103800;T:517279706;N:0", 944, null, null, null, 549431032, 411510218, 422103800, 517279706, 0, "ERX4273969", "ERS4808635", "ERA2764800", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "ont", "ont", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-07-05", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [9924, "ERR4326350", "ERX4273208", "ERS4808398", "ERP122761", "PRJEB39265", "RNA dynamics during zebrafish development", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183", "Other", "RNA dynamics during early zebrafish development", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, "430 LNA 6h rep1", "430 LNA 6h rep1", "SAMEA7047764", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569", null, null, null, null, null, null, null, null, "PromethION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "PromethION", null, "ERP122761", "PromethION sequencing", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", "JD-H8_PDBN059569.tar.gz", "nanopore", 722817654.0, 657296.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1", "0:1099.68", "A:206996491;C:157022109;G:155085437;T:203713617;N:0", 1099, null, null, null, 206996491, 157022109, 155085437, 203713617, 0, "ERX4273208", "ERS4808398", "ERA2764399", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "ont", "ont", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-07-05", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [9925, "ERR4335436", "ERX4282181", "ERS4818366", "ERP122761", "PRJEB39265", "RNA dynamics during zebrafish development", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183", "Other", "RNA dynamics during early zebrafish development", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, "WT 6h rep2", "WT 6h rep2", "JD W23 PRPN039928", null, "ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, null, null, null, null, "PromethION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "PromethION", null, "ERP122761", "PromethION sequencing", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", "JD-W23_PRPN039928.tar.gz", "nanopore", 1268761319.0, 1385621.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1", "0:915.66", "A:366823862;C:275507684;G:284634548;T:341795225;N:0", 915, null, null, null, 366823862, 275507684, 284634548, 341795225, 0, "ERX4282181", "ERS4818366", "ERA2769006", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "ont", "ont", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-07-05", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [9926, "ERR4321680", "ERX4268538", "ERS4808125", "ERP122761", "PRJEB39265", "RNA dynamics during zebrafish development", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183", "Other", "RNA dynamics during early zebrafish development", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, "WT 0h rep1", "WT 0h rep1", "JD A1 GDDN003032", null, "ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, null, null, null, null, "GridION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "GridION", null, "ERP122761", "GridION sequencing", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", "JD-A1_GDDN003032.tar.gz", "nanopore", 753417826.0, 698774.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1", "0:1078.20", "A:214525685;C:165042952;G:171160615;T:202688574;N:0", 1078, null, null, null, 214525685, 165042952, 171160615, 202688574, 0, "ERX4268538", "ERS4808125", "ERA2763718", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "ont", "ont", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-07-05", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [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. 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", "2874F22-1_210715_D00404_0538_BCD91CANXX_TCGACGTC-CTAAGCCT_L006_R1_001.fastq.gz", "fastq", 658093749.0, 12903799.0, "E MTAB 11083:2874F22 1 210715 D00404 0538 BCD91CANXX TCGACGTC CTAAGCCT L006", "0:51 1:0", "A:173355262;C:152464129;G:147489024;T:184739885;N:45449", 51, 0, null, null, 173355262, 152464129, 147489024, 184739885, 45449, "ERX6698608", "ERS8070397", "ERA6757553", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", "Friedrich Miescher Institute for Biomedical Research|European Nucleotide Archive", 1, 0.78328, null, 0.15147, null, 0.71289, null, 0.53671, 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"], [10238, "ERR7131170", "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. 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"], [11041, "ERR9995536", "ERX9536682", "ERS12521224", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "dRNA seq of 4hpf Zebrafish embryos", "Zebrafish dRNA 4hpf", "SAMEA110422854", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110422854|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:21:01Z|INSDC last update:2022 10 10T00:21:01Z|INSDC status:public|Submitter Id:Zebrafish dRNA 4hpf|common name:zebrafish|sample name:Zebrafish dRNA 4hpf", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 27 07 2022 11:41:43:673 3", "Zebrafish dRNA 4hpf", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|instrument model:PromethION", "PDBN042841_dRNA_4hpf.tar.gz", "nanopore", 772304625.0, 897768.0, "ena RUN TAB 27 07 2022 11:41:43:690 4", "0:860.25", "A:224977035;C:165273397;G:156659356;T:225394837;N:0", 860, null, null, null, 224977035, 165273397, 156659356, 225394837, 0, "ERX9536682", "ERS12521224", "ERA16500713", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25304, "SRR25793376", "SRX21515638", "SRS18742880", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes miR 144    adult", "miR 144 adult", null, "isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 1", "144 1 adult blood", "144 1 adult blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-144AL1_S10.fastq", "fastq", 781435052.0, 17368946.0, "DC 144AL1 S10.fastq", "0:44.99", "A:207445570;C:148430622;G:177122903;T:245179579;N:3256378", 44, null, null, null, 207445570, 148430622, 177122903, 245179579, 3256378, "SRX21515638", "SRS18742880", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.8759, null, 0.28126, null, 0.95051, null, 0.47905, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Adult", "Adult", "Blood", "Hematopoietic System"], [25305, "SRR25793377", "SRX21515637", "SRS18742882", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes Wild type   adult", "WT adult", null, "isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 3", "WT3 adult blood", "WT3 adult blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-WTA3_S6.fastq", "fastq", 601997398.0, 17290043.0, "DC WTA3 S6.fastq", "0:34.82", "A:136034449;C:142779447;G:177204517;T:134955264;N:11023721", 34, null, null, null, 136034449, 142779447, 177204517, 134955264, 11023721, "SRX21515637", "SRS18742882", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.32909, null, 0.08525, null, 0.95288, null, 0.60214, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Adult", "Adult", "Blood", "Hematopoietic System"], [25306, "SRR25793378", "SRX21515636", "SRS18742882", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes Wild type   adult", "WT adult", null, "isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 2", "WT2 adult blood", "WT2 adult blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-WTA2_S5.fastq", "fastq", 669871903.0, 17381581.0, "DC WTA2 S5.fastq", "0:38.54", "A:169704437;C:140964096;G:160484620;T:189596855;N:9121895", 38, null, null, null, 169704437, 140964096, 160484620, 189596855, 9121895, "SRX21515636", "SRS18742882", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.69865, null, 0.19099, null, 0.93432, null, 0.47502, null, 68, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Adult", "Adult", "Blood", "Hematopoietic System"], [25307, "SRR25793379", "SRX21515635", "SRS18742882", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes Wild type   adult", "WT adult", null, "isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 1", "WT1 adult blood", "WT1 adult blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-WTA1_S4.fastq", "fastq", 824193699.0, 17465379.0, "DC WTA1 S4.fastq", "0:47.19", "A:209553199;C:169966117;G:194322860;T:244145525;N:6205998", 47, null, null, null, 209553199, 169966117, 194322860, 244145525, 6205998, "SRX21515635", "SRS18742882", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.76241, null, 0.25975, null, 0.94619, null, 0.50211, null, 66, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Adult", "Adult", "Blood", "Hematopoietic System"], [25308, "SRR25793380", "SRX21515634", "SRS18742881", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes miR 144    embryo", "miR 144 embryo", null, "isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 3", "144 3 embryo blood", "144 3 embryo blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-144EL3_S18.fastq", "fastq", 687309797.0, 17039739.0, "DC 144EL3 S18.fastq", "0:40.34", "A:159186558;C:130452893;G:155820002;T:181676510;N:60173834", 40, null, null, null, 159186558, 130452893, 155820002, 181676510, 60173834, "SRX21515634", "SRS18742881", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.52966, null, 0.16941, null, 0.97615, null, 0.58418, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [25309, "SRR25793381", "SRX21515633", "SRS18742881", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes miR 144    embryo", "miR 144 embryo", null, "isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 2", "144 2 embryo blood", "144 2 embryo blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-144EL2_S17.fastq", "fastq", 495318731.0, 14459195.0, "DC 144EL2 S17.fastq", "0:34.26", "A:110392869;C:106378418;G:128881687;T:107956679;N:41709078", 34, null, null, null, 110392869, 106378418, 128881687, 107956679, 41709078, "SRX21515633", "SRS18742881", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.32147, null, 0.04496, null, 0.97569, null, 0.58512, null, 31, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [25310, "SRR25793382", "SRX21515632", "SRS18742881", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes miR 144    embryo", "miR 144 embryo", null, "isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 1", "144 1 embryo blood", "144 1 embryo blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-144EL1_S16.fastq", "fastq", 974854100.0, 20079553.0, "DC 144EL1 S16.fastq", "0:48.55", "A:233861010;C:192987350;G:215192262;T:269960344;N:62853134", 48, null, null, null, 233861010, 192987350, 215192262, 269960344, 62853134, "SRX21515632", "SRS18742881", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.77953, null, 0.18084, null, 0.90905, null, 0.74157, null, 75, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [25311, "SRR25793383", "SRX21515631", "SRS18742879", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes Wild type   embryo", "WT embryo", null, "isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 3", "WT3 embryo blood", "WT3 embryo blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-WTE3_S15.fastq", "fastq", 657139116.0, 15618072.0, "DC WTE3 S15.fastq", "0:42.08", "A:154495614;C:122942896;G:147719345;T:179403193;N:52578068", 42, null, null, null, 154495614, 122942896, 147719345, 179403193, 52578068, "SRX21515631", "SRS18742879", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.56358, null, 0.19381, null, 0.96757, null, 0.6115, null, 76, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [25312, "SRR25793384", "SRX21515630", "SRS18742880", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes miR 144    adult", "miR 144 adult", null, "isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 3", "144 3 adult blood", "144 3 adult blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-144AL3_S12.fastq", "fastq", 498938612.0, 14861511.0, "DC 144AL3 S12.fastq", "0:33.57", "A:137243823;C:96735877;G:109220779;T:152042235;N:3695898", 33, null, null, null, 137243823, 96735877, 109220779, 152042235, 3695898, "SRX21515630", "SRS18742880", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.82213, null, 0.16617, null, 0.95053, null, 0.46386, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Adult", "Adult", "Blood", "Hematopoietic System"], [25313, "SRR25793385", "SRX21515629", "SRS18742880", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes miR 144    adult", "miR 144 adult", null, "isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 2", "144 2 adult blood", "144 2 adult blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-144AL2_S11.fastq", "fastq", 497890134.0, 10636306.0, "DC 144AL2 S11.fastq", "0:46.81", "A:134598214;C:94036725;G:109501897;T:158719603;N:1033695", 46, null, null, null, 134598214, 94036725, 109501897, 158719603, 1033695, "SRX21515629", "SRS18742880", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.88496, null, 0.29132, null, 0.96002, null, 0.53343, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Adult", "Adult", "Blood", "Hematopoietic System"], [25314, "SRR25793386", "SRX21515628", "SRS18742879", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes Wild type   embryo", "WT embryo", null, "isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 2", "WT2 embryo blood", "WT2 embryo blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-WTE2_S14.fastq", "fastq", 250958009.0, 9755304.0, "DC WTE2 S14.fastq", "0:25.73", "A:43225839;C:41823862;G:54150092;T:43159724;N:68598492", 25, null, null, null, 43225839, 41823862, 54150092, 43159724, 68598492, "SRX21515628", "SRS18742879", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.34114, null, 0.05466, null, 0.96664, null, 0.54625, null, 47, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [25315, "SRR25793387", "SRX21515627", "SRS18742879", "SRP457465", "PRJNA1010662", "The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.", "PRJNA1010662", "Other", "Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.", null, null, null, "RNA seq Erythrocytes Wild type   embryo", "WT embryo", null, "isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 1", "WT1 embryo blood", "WT1 embryo blood", "Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "DC-WTE1_S13.fastq", "fastq", 816518564.0, 19556325.0, "DC WTE1 S13.fastq", "0:41.75", "A:187091550;C:151287428;G:179967901;T:221475884;N:76695801", 41, null, null, null, 187091550, 151287428, 179967901, 221475884, 76695801, "SRX21515627", "SRS18742879", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.61681, null, 0.1874, null, 0.95101, null, 0.56879, null, 29, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [26499, "SRR26031755", "SRX21749012", "SRS18856550", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "RNAseq hand2FACS rtf1MO 3", null, "strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 14|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos", "M3", "MO3", "NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "RNAseq_hand2FACS_rtf1MO_3.fastq", "fastq", 793876754.0, 15197870.0, "RNAseq hand2FACS rtf1MO 3.fastq", "0:52.24", "A:208793415;C:174763420;G:174630814;T:235479388;N:209717", 52, null, null, null, 208793415, 174763420, 174630814, 235479388, 209717, "SRX21749012", "SRS18856550", "SRA1709841", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.88868, null, 0.1097, null, 0.77644, null, 0.51136, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [26500, "SRR26031756", "SRX21749011", "SRS18856545", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "RNAseq hand2FACS rtf1MO 2", null, "strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 07|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos", "M2", "MO2", "NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "RNAseq_hand2FACS_rtf1MO_2.fastq", "fastq", 864787205.0, 16568310.0, "RNAseq hand2FACS rtf1MO 2.fastq", "0:52.20", "A:227648729;C:189720880;G:190025417;T:257026454;N:365725", 52, null, null, null, 227648729, 189720880, 190025417, 257026454, 365725, "SRX21749011", "SRS18856545", "SRA1709841", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.87433, null, 0.10781, null, 0.77366, null, 0.50792, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [26501, "SRR26031757", "SRX21749010", "SRS18856549", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "RNAseq hand2FACS rtf1MO 1", null, "strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 03 04|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos", "M1", "MO1", "NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "RNAseq_hand2FACS_rtf1MO_1.fastq", "fastq", 821983134.0, 15737564.0, "RNAseq hand2FACS rtf1MO 1.fastq", "0:52.23", "A:216610704;C:179969953;G:180145537;T:245093230;N:163710", 52, null, null, null, 216610704, 179969953, 180145537, 245093230, 163710, "SRX21749010", "SRS18856549", "SRA1709841", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.88099, null, 0.09837, null, 0.78007, null, 0.50262, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [26502, "SRR26031758", "SRX21749009", "SRS18856546", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "RNAseq hand2FACS control 3", null, "strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 02 26|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos", "C3", "CTL3", "NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "RNAseq_hand2FACS_control_3.fastq", "fastq", 880285441.0, 16931477.0, "RNAseq hand2FACS control 3.fastq", "0:51.99", "A:233959122;C:192477087;G:190893530;T:262700285;N:255417", 51, null, null, null, 233959122, 192477087, 190893530, 262700285, 255417, "SRX21749009", "SRS18856546", "SRA1709841", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.90285, null, 0.10232, null, 0.76982, null, 0.50837, null, 53, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [26503, "SRR26031759", "SRX21749008", "SRS18856548", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "RNAseq hand2FACS control 2", null, "strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 12 19|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos", "C2", "CTL2", "NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "RNAseq_hand2FACS_control_2.fastq", "fastq", 317458963.0, 6417814.0, "RNAseq hand2FACS control 2.fastq", "0:49.47", "A:83925064;C:70621123;G:68872886;T:93923129;N:116761", 49, null, null, null, 83925064, 70621123, 68872886, 93923129, 116761, "SRX21749008", "SRS18856548", "SRA1709841", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.85587, null, 0.08493, null, 0.75558, null, 0.51678, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [26504, "SRR26031760", "SRX21749007", "SRS18856543", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "RNAseq hand2FACS control 1", null, "strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 11 29|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos", "C1", "CTL1", "NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP459729", null, null, "RNAseq_hand2FACS_control_1.fastq", "fastq", 448273888.0, 9055865.0, "RNAseq hand2FACS control 1.fastq", "0:49.50", "A:119317727;C:99863109;G:96352533;T:132659621;N:80898", 49, null, null, null, 119317727, 99863109, 96352533, 132659621, 80898, "SRX21749007", "SRS18856543", "SRA1709841", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.88622, null, 0.09573, null, 0.76086, null, 0.42689, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28538, "SRR26395012", "SRX22100922", "SRS19166048", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "50% epiboly Iso seq", null, "strain:AB x India|age:5.3 hpf|dev stage:50% epiboly|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "PacBio Iso seq of zebrafish: 50% epiboly", "DR 010", "DR 010", "Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP466518", null, null, "50epiboly.ccs.fq.gz", "fastq", 6994871304.0, 1739615.0, "50epiboly.ccs.fq.gz", "0:4020.93", "A:1886646970;C:1618863911;G:1609321304;T:1880039119;N:0", 4020, null, null, null, 1886646970, 1618863911, 1609321304, 1880039119, 0, "SRX22100922", "SRS19166048", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 1, 0.2059, null, 0.00164, null, 0.92101, null, 0.06119, null, 3367, null, "T", null, "long read", "pacbio", "pacbio_modern", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28539, "SRR26395013", "SRX22100921", "SRS19166047", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "zfs:0000015 Iso seq", null, "strain:AB x India|age:4.7 hpf|dev stage:zfs:0000015|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "PacBio Iso seq of zebrafish: zfs:0000015", "DR 009", "DR 009", "Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP466518", null, null, "30epiboly.ccs.fq.gz", "fastq", 5233736965.0, 1358516.0, "zfs:0000015.ccs.fq.gz", "0:3852.54", "A:1425421240;C:1199630062;G:1191034759;T:1417650904;N:0", 3852, null, null, null, 1425421240, 1199630062, 1191034759, 1417650904, 0, "SRX22100921", "SRS19166047", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 1, 0.40862, null, 0.00581, null, 0.86123, null, 0.47684, null, 3440, null, "T", null, "long read", "pacbio", "pacbio_modern", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28540, "SRR26395014", "SRX22100920", "SRS19166046", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "dome Iso seq", null, "strain:AB x India|age:4.3 hpf|dev stage:dome|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "PacBio Iso seq of zebrafish: dome", "DR 008", "DR 008", "Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. 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The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. 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Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "oblong Iso seq", null, "strain:AB x India|age:3.7 hpf|dev stage:oblong|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "PacBio Iso seq of zebrafish: oblong", "DR 006", "DR 006", "Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. 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