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501 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "Oligo-dT" and experiment.platform = "ILLUMINA"

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tissue_curation >10

devstage_curation 10

devstage_curation_coarse 4

technology 3

experiment.library_source 2

experiment.platform 1

  • ILLUMINA · 501 ✖

experiment.library_strategy 1

experiment.library_selection 1

  • Oligo-dT · 501 ✖

experiment.library_layout 1

  • SINGLE · 501 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
3759 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     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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   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       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   0.10666   0.73176   0.50978   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3760 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. 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     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                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8 vbu12 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu12_GTGAAA_L008_R1_001.fastq.gz fastq 1449181835.0 14348335.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8 0:101 A:399518584;C:327615685;G:323868050;T:397240465;N:939051 101       399518584 327615685 323868050 397240465 939051 ERX1365624 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95893   0.09315   0.73464   0.48744   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3761 3761 ERR1294277 ERX1365623 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     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                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7 vbu11 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu11_GTCCGC_L008_R1_001.fastq.gz fastq 1455235169.0 14408269.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7 0:101 A:392100064;C:337980617;G:331091626;T:393178582;N:884280 101       392100064 337980617 331091626 393178582 884280 ERX1365623 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95485   0.08016   0.72845   0.47549   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3762 3762 ERR1294276 ERX1365622 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. 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     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                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6 ve13 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve13_CCGTCC_L008_R1_001.fastq.gz fastq 1029294030.0 10191030.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6 0:101 A:284612731;C:231451012;G:228443320;T:284135536;N:651431 101       284612731 231451012 228443320 284135536 651431 ERX1365622 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.93287   0.10726   0.72585   0.4913   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3763 3763 ERR1294275 ERX1365621 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. 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     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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   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       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   0.09489   0.73093   0.48493   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3764 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. 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     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                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4 ve11 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve11_AGTTCC_L008_R1_001.fastq.gz fastq 2117238861.0 20962761.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4 0:101 A:591654664;C:469803769;G:462550117;T:591863795;N:1366516 101       591654664 469803769 462550117 591863795 1366516 ERX1365620 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.93146   0.09666   0.73501   0.48749   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3765 3765 ERR1294273 ERX1365619 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. 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     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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   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       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   0.1036   0.72474   0.48261   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3766 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. 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     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                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2 wt2 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt2_CTTGTA_L008_R1_001.fastq.gz fastq 2093443463.0 20727163.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2 0:101 A:607582034;C:442802229;G:437957089;T:603752294;N:1349817 101       607582034 442802229 437957089 603752294 1349817 ERX1365618 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.94792   0.10892   0.73277   0.51067   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3767 3767 ERR1294271 ERX1365617 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. 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     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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   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       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   0.13032   0.73669   0.50473   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
5879 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   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                 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’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. Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   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     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   0.27583   0.75398   0.55917   75   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
5880 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   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                 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’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. Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   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     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   0.2509   0.79005   0.54852   75   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
5881 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   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                 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’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. Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   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     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   0.20554   0.76301   0.55753   74   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
5882 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   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                 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’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. Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina MiSeq   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     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   0.21561   0.77477   0.53919   73   B   usable mapping rate illumina miseq full_length poly_a nebnext bulk unknown unknown   Japan 2016-12-15 Larval Larval Heart Cardiovascular System
9361 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   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. 3µg 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                 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. 3µg 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   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     455444321 410713896 385640226 503155736 9761 ERX3014407 ERS2994081 ERA1697296 European Nucleotide Archive European Nucleotide Archive 1 0.94351   0.11595   0.67483   0.48762   73   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Unknown 2018-12-18 Larval Larval Embryo Imprecise All anatomical structures
9362 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   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. 3µg 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                 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. 3µg 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   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     424378341 380806325 358128992 467779945 9260 ERX3014406 ERS2994080 ERA1697296 European Nucleotide Archive European Nucleotide Archive 1 0.94332   0.11797   0.67596   0.48847   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Unknown 2018-12-18 Larval Larval Embryo Imprecise All anatomical structures
9363 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   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. 3µg 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                 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. 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. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1 RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   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_DMSO_2_R1.fastq.gz fastq 1811573293.0 24316929.0 E MTAB 7283:DMSO 2 0:74.50 1:0 A:470888315;C:423635861;G:396796840;T:520242179;N:10098 74 0     470888315 423635861 396796840 520242179 10098 ERX3014405 ERS2994079 ERA1697296 European Nucleotide Archive European Nucleotide Archive 1 0.94219   0.12305   0.67184   0.47704   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Unknown 2018-12-18 Larval Larval Embryo Imprecise All anatomical structures
9364 9364 ERR3011944 ERX3014404 ERS2994078 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   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. 3µg 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                 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. 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. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1 RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   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_DMSO_1_R1.fastq.gz fastq 1609807409.0 21611475.0 E MTAB 7283:DMSO 1 0:74.49 1:0 A:420253680;C:374436301;G:352526427;T:462581933;N:9068 74 0     420253680 374436301 352526427 462581933 9068 ERX3014404 ERS2994078 ERA1697296 European Nucleotide Archive European Nucleotide Archive 1 0.94094   0.12292   0.67006   0.48442   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Unknown 2018-12-18 Larval Larval Embryo Imprecise All anatomical structures
9365 9365 ERR3011943 ERX3014403 ERS2994077 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   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. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina Cyproter1 2 SAMEA5186578 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:SAMEA5186578|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:Cyproter1 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:Cyproter1 2|scientific name:Danio rerio|strain:ins bns102                 NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants E MTAB 7283:Cyproterone 2 s Cyproterone 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. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina Experimental Factor: compound:cyproter1|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   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_Cyproterone_2_R1.fastq.gz fastq 1823142918.0 24468337.0 E MTAB 7283:Cyproterone 2 0:74.51 1:0 A:469387174;C:428783310;G:403791044;T:521171021;N:10369 74 0     469387174 428783310 403791044 521171021 10369 ERX3014403 ERS2994077 ERA1697296 European Nucleotide Archive European Nucleotide Archive 1 0.9432   0.11718   0.67389   0.4768   74   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Unknown 2018-12-18 Larval Larval Embryo Imprecise All anatomical structures
9366 9366 ERR3011942 ERX3014402 ERS2994076 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   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. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina Cyproter1 1 SAMEA5186577 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:SAMEA5186577|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:Cyproter1 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:Cyproter1 1|scientific name:Danio rerio|strain:ins bns102                 NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants E MTAB 7283:Cyproterone 1 s Cyproterone 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. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina Experimental Factor: compound:cyproter1|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   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_Cyproterone_1_R1.fastq.gz fastq 1901027130.0 25512731.0 E MTAB 7283:Cyproterone 1 0:74.51 1:0 A:487302419;C:449208827;G:422183780;T:542321577;N:10527 74 0     487302419 449208827 422183780 542321577 10527 ERX3014402 ERS2994076 ERA1697296 European Nucleotide Archive European Nucleotide Archive 1 0.94427   0.11318   0.67294   0.47183   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Unknown 2018-12-18 Larval Larval Embryo Imprecise All anatomical structures
10186 10186 ERR6212423 ERX5847531 ERS7094943 ERP130388 PRJEB46176 scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord E-MTAB-10379_3 Transcriptome Analysis To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08   Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Naive SAMEA9361876 University Of Edinburgh ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK                 Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord E MTAB 10379 3:Naive p Naive p scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Experimental Factor: injury:n1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   ERP130388 Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08 Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz fastq fastq fastq 60168324125.0 481346593.0 E MTAB 10379 3:Naive 0:8 1:27 2:90 A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241 8 27 90   12424400694 9366563781 10029312355 11497237299 3679241 ERX5847531 ERS7094943 ERA5186263 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 1 0.94834   0.09482   0.802   0.5277   90   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   United Kingdom 2021-07-08 Larval Larval Multi-tissue Multi-system
10187 10187 ERR6212422 ERX5847530 ERS7094942 ERP130388 PRJEB46176 scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord E-MTAB-10379_3 Transcriptome Analysis To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08   Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Lesi1d SAMEA9361875 University Of Edinburgh ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK                 Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord E MTAB 10379 3:Lesioned p Lesioned p scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Experimental Factor: injury:spinal cord lesion RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   ERP130388 Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08 Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz fastq fastq fastq 61701873000.0 493614984.0 E MTAB 10379 3:Lesioned 0:8 1:27 2:90 A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277 8 27 90   12952533019 9222397450 9920185920 12326470894 3761277 ERX5847530 ERS7094942 ERA5186263 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 1 0.93082   0.10862   0.80302   0.54924   90   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   United Kingdom 2021-07-08 Larval Larval Multi-tissue Multi-system
10237 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   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                 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   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     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   0.15147   0.71289   0.53671   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10238 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   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                 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   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     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   0.15054   0.70897   0.5322   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10239 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   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                 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   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     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   0.15593   0.75828   0.51858   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10240 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   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                 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   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     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   0.15634   0.75909   0.51346   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10241 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   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                 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   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     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   0.19774   0.74576   0.52117   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10242 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   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                 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   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     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   0.19902   0.74517   0.52618   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10243 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   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                 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   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     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   0.17309   0.71003   0.53696   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10244 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   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                 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   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     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   0.17497   0.71078   0.53767   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10245 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   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                 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   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     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   0.11592   0.82615   0.5252   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10246 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   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                 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   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     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   0.1152   0.8258   0.53305   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10247 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   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                 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   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     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   0.2048   0.75923   0.52828   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10248 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   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                 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   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     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   0.20314   0.75852   0.52949   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10249 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   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                 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   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     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   0.16001   0.71467   0.53352   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10250 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   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                 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   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     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   0.15963   0.71569   0.53038   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10251 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   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                 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   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     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   0.18123   0.77193   0.53313   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10252 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   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                 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   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     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   0.18101   0.77141   0.53601   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10253 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   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                 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   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     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   0.1953   0.76292   0.5395   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10254 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   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                 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   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     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   0.19726   0.76299   0.54099   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10255 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   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                 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   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     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   0.17457   0.71934   0.53563   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10256 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   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                 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   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     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   0.17387   0.72153   0.54149   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10257 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   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                 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   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     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   0.18671   0.76047   0.52398   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10258 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   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                 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   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     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   0.18813   0.76378   0.5258   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10259 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   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                 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   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     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   0.1977   0.77193   0.53352   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10260 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   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                 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   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     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   0.20019   0.7707   0.52174   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10261 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   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                 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   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     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   0.2508   0.71299   0.53379   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10262 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   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                 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   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     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   0.25356   0.71344   0.53081   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10263 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   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                 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   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     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   0.20794   0.81223   0.52529   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10264 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   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                 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   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     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   0.20724   0.80468   0.52791   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10265 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   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                 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   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     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   0.19842   0.74986   0.53363   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10266 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   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                 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   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     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   0.19727   0.74805   0.53092   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10267 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   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                 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   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     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   0.15219   0.71277   0.52461   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10268 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   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                 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   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     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   0.15444   0.7151   0.52585   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10269 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   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                 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   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     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   0.17778   0.76899   0.52957   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10270 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   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                 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   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     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   0.17896   0.77076   0.52835   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10271 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   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                 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   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     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   0.21547   0.75588   0.53853   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10272 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   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                 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   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     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   0.21684   0.75621   0.53787   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10273 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   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                 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   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     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   0.17302   0.72281   0.54315   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10274 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   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                 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   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     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   0.17082   0.72196   0.54505   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10275 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   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                 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   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     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   0.21407   0.76104   0.52713   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10276 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   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                 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   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     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   0.21431   0.761   0.5071   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10277 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   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                 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   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     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   0.18905   0.73241   0.52347   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10278 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   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                 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   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     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   0.18885   0.73156   0.51691   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10279 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   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                 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   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     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   0.17703   0.72614   0.53483   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10280 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   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                 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   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     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   0.17699   0.726   0.53711   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10281 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   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                 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   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     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   0.18489   0.75345   0.52316   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10282 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   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                 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   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     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   0.18414   0.75375   0.52317   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10283 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   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                 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   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     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   0.21674   0.73359   0.52207   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
10284 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   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                 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   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     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   0.21645   0.73494   0.50761   51   B   usable mapping rate illumina hiseq_era unknown poly_a nextera sc single_cell_plate smartseq   Switzerland 2021-12-01 Adult Adult Brain Nervous System
25304 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.       RNA seq Erythrocytes miR 144 adult miR 144 adult   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       207445570 148430622 177122903 245179579 3256378 SRX21515638 SRS18742880 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.8759   0.28126   0.95051   0.47905   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25305 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.       RNA seq Erythrocytes Wild type adult WT adult   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       136034449 142779447 177204517 134955264 11023721 SRX21515637 SRS18742882 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.32909   0.08525   0.95288   0.60214   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25306 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.       RNA seq Erythrocytes Wild type adult WT adult   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       169704437 140964096 160484620 189596855 9121895 SRX21515636 SRS18742882 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.69865   0.19099   0.93432   0.47502   68   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25307 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.       RNA seq Erythrocytes Wild type adult WT adult   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       209553199 169966117 194322860 244145525 6205998 SRX21515635 SRS18742882 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.76241   0.25975   0.94619   0.50211   66   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25308 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.       RNA seq Erythrocytes miR 144 embryo miR 144 embryo   isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       159186558 130452893 155820002 181676510 60173834 SRX21515634 SRS18742881 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.52966   0.16941   0.97615   0.58418   61   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25309 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.       RNA seq Erythrocytes miR 144 embryo miR 144 embryo   isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       110392869 106378418 128881687 107956679 41709078 SRX21515633 SRS18742881 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.32147   0.04496   0.97569   0.58512   31   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25310 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.       RNA seq Erythrocytes miR 144 embryo miR 144 embryo   isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       233861010 192987350 215192262 269960344 62853134 SRX21515632 SRS18742881 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.77953   0.18084   0.90905   0.74157   75   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25311 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.       RNA seq Erythrocytes Wild type embryo WT embryo   isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       154495614 122942896 147719345 179403193 52578068 SRX21515631 SRS18742879 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.56358   0.19381   0.96757   0.6115   76   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25312 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.       RNA seq Erythrocytes miR 144 adult miR 144 adult   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       137243823 96735877 109220779 152042235 3695898 SRX21515630 SRS18742880 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.82213   0.16617   0.95053   0.46386   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25313 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.       RNA seq Erythrocytes miR 144 adult miR 144 adult   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       134598214 94036725 109501897 158719603 1033695 SRX21515629 SRS18742880 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.88496   0.29132   0.96002   0.53343   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25314 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.       RNA seq Erythrocytes Wild type embryo WT embryo   isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       43225839 41823862 54150092 43159724 68598492 SRX21515628 SRS18742879 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.34114   0.05466   0.96664   0.54625   47   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25315 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.       RNA seq Erythrocytes Wild type embryo WT embryo   isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     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       187091550 151287428 179967901 221475884 76695801 SRX21515627 SRS18742879 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.61681   0.1874   0.95101   0.56879   29   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
26499 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.         RNAseq hand2FACS rtf1MO 3   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                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     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       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   0.1097   0.77644   0.51136   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26500 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.         RNAseq hand2FACS rtf1MO 2   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                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     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       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   0.10781   0.77366   0.50792   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26501 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.         RNAseq hand2FACS rtf1MO 1   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                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     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       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   0.09837   0.78007   0.50262   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26502 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.         RNAseq hand2FACS control 3   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                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     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       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   0.10232   0.76982   0.50837   53   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26503 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.         RNAseq hand2FACS control 2   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                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     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       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   0.08493   0.75558   0.51678   50   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
26504 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.         RNAseq hand2FACS control 1   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                 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     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 3000   SRP459729     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       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   0.09573   0.76086   0.42689   49   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-09-11 Segmentation Embryo Embryo Imprecise All anatomical structures
29259 29259 SRR27336917 SRX23013778 SRS19977075 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep2 miR214 PaternalKO gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A11 miR214 PaternalKO gonads 31dpf rep2 miR214 PaternalKO gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep2.fastq.gz fastq 2327996832.0 27714248.0 miR214 PaternalKO gonads 31dpf rep2.fastq.gz 0:84 A:602135965;C:552786494;G:537368428;T:635697339;N:8606 84       602135965 552786494 537368428 635697339 8606 SRX23013778 SRS19977075 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95369   0.06146   0.69203   0.47259   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29260 29260 SRR27336918 SRX23013777 SRS19977074 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep1 miR214 PaternalKO gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A10 miR214 PaternalKO gonads 31dpf rep1 miR214 PaternalKO gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz fastq 2500978452.0 29773553.0 miR214 PaternalKO gonads 31dpf rep1.fastq.gz 0:84 A:646162933;C:593855971;G:578265372;T:682684551;N:9625 84       646162933 593855971 578265372 682684551 9625 SRX23013777 SRS19977074 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95147   0.05972   0.69071   0.47043   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29261 29261 SRR27336919 SRX23013776 SRS19977073 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep4 miR214 maternalHET gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep4|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A9 miR214 maternalHET gonads 31dpf rep4 miR214 maternalHET gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep4.fastq.gz fastq 2365480908.0 28160487.0 miR214 maternalHET gonads 31dpf rep4.fastq.gz 0:84 A:613121312;C:560582165;G:549338096;T:642429834;N:9501 84       613121312 560582165 549338096 642429834 9501 SRX23013776 SRS19977073 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95304   0.05342   0.7108   0.46822   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29262 29262 SRR27336920 SRX23013775 SRS19977072 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep3 miR214 maternalHET gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep3|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A8 miR214 maternalHET gonads 31dpf rep3 miR214 maternalHET gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep3.fastq.gz fastq 2537794644.0 30211841.0 miR214 maternalHET gonads 31dpf rep3.fastq.gz 0:84 A:658687178;C:600742464;G:585643169;T:692712057;N:9776 84       658687178 600742464 585643169 692712057 9776 SRX23013775 SRS19977072 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95177   0.06701   0.68195   0.47393   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29263 29263 SRR27336921 SRX23013774 SRS19977071 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep2 miR214 maternalHET gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep2|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A7 miR214 maternalHET gonads 31dpf rep2 miR214 maternalHET gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep2.fastq.gz fastq 2417384424.0 28778386.0 miR214 maternalHET gonads 31dpf rep2.fastq.gz 0:84 A:625935186;C:574179061;G:560498085;T:656762980;N:9112 84       625935186 574179061 560498085 656762980 9112 SRX23013774 SRS19977071 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95259   0.05852   0.6981   0.47435   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29264 29264 SRR27336922 SRX23013773 SRS19977070 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep1 miR214 maternalHET gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep1|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A6 miR214 maternalHET gonads 31dpf rep1 miR214 maternalHET gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep1.fastq.gz fastq 2330886180.0 27748645.0 miR214 maternalHET gonads 31dpf rep1.fastq.gz 0:84 A:601589571;C:554105326;G:542789267;T:632393158;N:8858 84       601589571 554105326 542789267 632393158 8858 SRX23013773 SRS19977070 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95338   0.05239   0.71366   0.47291   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29265 29265 SRR27336923 SRX23013772 SRS19977069 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep4 miR214 maternalKO gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A5 miR214 maternalKO gonads 31dpf rep4 miR214 maternalKO gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep4.fastq.gz fastq 2340233784.0 27859926.0 miR214 maternalKO gonads 31dpf rep4.fastq.gz 0:84 A:606735187;C:553647808;G:539865459;T:639976430;N:8900 84       606735187 553647808 539865459 639976430 8900 SRX23013772 SRS19977069 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95406   0.06415   0.68225   0.47695   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29266 29266 SRR27336924 SRX23013771 SRS19977068 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep3 miR214 maternalKO gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A4 miR214 maternalKO gonads 31dpf rep3 miR214 maternalKO gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep3.fastq.gz fastq 2058505512.0 24506018.0 miR214 maternalKO gonads 31dpf rep3.fastq.gz 0:84 A:537425814;C:485664494;G:471526682;T:563881213;N:7309 84       537425814 485664494 471526682 563881213 7309 SRX23013771 SRS19977068 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95296   0.06728   0.69266   0.47627   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29267 29267 SRR27336925 SRX23013770 SRS19977067 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep4 miR214 PaternalHET gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep4|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A17 miR214 PaternalHET gonads 31dpf rep4 miR214 PaternalHET gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep4.fastq.gz fastq 3001613328.0 35733492.0 miR214 PaternalHET gonads 31dpf rep4.fastq.gz 0:84 A:778860501;C:711155422;G:688784969;T:822801157;N:11279 84       778860501 711155422 688784969 822801157 11279 SRX23013770 SRS19977067 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95361   0.05653   0.7051   0.48382   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29268 29268 SRR27336926 SRX23013769 SRS19977066 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep3 miR214 PaternalHET gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A16 miR214 PaternalHET gonads 31dpf rep3 miR214 PaternalHET gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep3.fastq.gz fastq 3053630664.0 36352746.0 miR214 PaternalHET gonads 31dpf rep3.fastq.gz 0:84 A:785219727;C:726431662;G:713454025;T:828513556;N:11694 84       785219727 726431662 713454025 828513556 11694 SRX23013769 SRS19977066 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95309   0.04588   0.71997   0.46447   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29269 29269 SRR27336927 SRX23013768 SRS19977065 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep2 miR214 PaternalHET gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A15 miR214 PaternalHET gonads 31dpf rep2 miR214 PaternalHET gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep2.fastq.gz fastq 3063695208.0 36472562.0 miR214 PaternalHET gonads 31dpf rep2.fastq.gz 0:84 A:784924646;C:728941687;G:720847462;T:828969510;N:11903 84       784924646 728941687 720847462 828969510 11903 SRX23013768 SRS19977065 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95413   0.04739   0.71936   0.4704   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29270 29270 SRR27336928 SRX23013767 SRS19977064 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep1 miR214 PaternalHET gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A14 miR214 PaternalHET gonads 31dpf rep1 miR214 PaternalHET gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep1.fastq.gz fastq 2699154024.0 32132786.0 miR214 PaternalHET gonads 31dpf rep1.fastq.gz 0:84 A:694174797;C:642049572;G:627991562;T:734927762;N:10331 84       694174797 642049572 627991562 734927762 10331 SRX23013767 SRS19977064 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95518   0.05525   0.70285   0.47695   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29271 29271 SRR27336929 SRX23013766 SRS19977063 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep4 miR214 PaternalKO gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A13 miR214 PaternalKO gonads 31dpf rep4 miR214 PaternalKO gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep4.fastq.gz fastq 2514248016.0 29931524.0 miR214 PaternalKO gonads 31dpf rep4.fastq.gz 0:84 A:648908956;C:598837726;G:580002743;T:686488678;N:9913 84       648908956 598837726 580002743 686488678 9913 SRX23013766 SRS19977063 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.94978   0.06951   0.67896   0.47686   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System

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