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38 rows where experiment.library_selection = "Inverse rRNA", experiment.library_strategy = "RNA-Seq" and technology = "bulk"

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tissue_curation_coarse 3

tissue_curation 3

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

technology 1

  • bulk · 38 ✖

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 38 ✖

experiment.library_source 1

experiment.library_selection 1

  • Inverse rRNA · 38 ✖
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
9812 9812 ERR3931362 ERX3938952 ERS4329529 ERP120057 PRJEB36819 Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E-MTAB-8800 Transcriptome Analysis Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05   Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. WKM 7 ED SAMEA6565186 Institute of Molecular Genetics of the Czech Academy of Sciences ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565186|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 ED                 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E MTAB 8800:WKM 7 ED s WKM 7 ED s Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC Inverse rRNA SINGLE ILLUMINA NextSeq 500   ERP120057 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 10_WKM_7_ED.fastq.gz fastq 3603783627.0 47724788.0 E MTAB 8800:WKM 7 ED 0:75.51 1:0 A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509 75 0     730277817 1059558661 1006087781 807771859 87509 ERX3938952 ERS4329529 ERA2383450 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 1 0.96114   0.20335   0.83798   0.76524   76   B   usable mapping rate illumina nextseq full_length rrna_depletion smarter bulk bulk bulk   Czech Republic 2021-12-31 Adult Adult Multi-tissue Multi-system
9813 9813 ERR3931361 ERX3938951 ERS4329528 ERP120057 PRJEB36819 Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E-MTAB-8800 Transcriptome Analysis Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05   Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. WKM 7 EaD SAMEA6565185 Institute of Molecular Genetics of the Czech Academy of Sciences ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565185|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 EaD                 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E MTAB 8800:WKM 7 EaD s WKM 7 EaD s Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. Experimental Factor: stimulus:kit ligand RNA-Seq TRANSCRIPTOMIC Inverse rRNA SINGLE ILLUMINA NextSeq 500   ERP120057 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 11_WKM_7_EaD_1.fastq.gz fastq 3127207407.0 41417754.0 E MTAB 8800:WKM 7 EaD 0:75.50 1:0 A:618290483;C:948661192;G:891134088;T:669046822;N:74822 75 0     618290483 948661192 891134088 669046822 74822 ERX3938951 ERS4329528 ERA2383450 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 1 0.96441   0.20171   0.85427   0.75425   76   B   usable mapping rate illumina nextseq full_length rrna_depletion smarter bulk bulk bulk   Czech Republic 2021-12-31 Adult Adult Multi-tissue Multi-system
9814 9814 ERR3931360 ERX3938950 ERS4329527 ERP120057 PRJEB36819 Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E-MTAB-8800 Transcriptome Analysis Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05   Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. WKM 5 ED SAMEA6565184 Institute of Molecular Genetics of the Czech Academy of Sciences ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565184|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 ED                 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E MTAB 8800:WKM 5 ED s WKM 5 ED s Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC Inverse rRNA SINGLE ILLUMINA NextSeq 500   ERP120057 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 8_WKM_5_ED.fastq.gz fastq 3762435507.0 49825705.0 E MTAB 8800:WKM 5 ED 0:75.51 1:0 A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573 75 0     760573477 1107794761 1060998015 832975681 93573 ERX3938950 ERS4329527 ERA2383450 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 1 0.96233   0.20628   0.84141   0.73601   75   B   usable mapping rate illumina nextseq full_length rrna_depletion smarter bulk bulk bulk   Czech Republic 2021-12-31 Adult Adult Multi-tissue Multi-system
9815 9815 ERR3931359 ERX3938949 ERS4329526 ERP120057 PRJEB36819 Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E-MTAB-8800 Transcriptome Analysis Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05   Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. WKM 5 EaD SAMEA6565183 Institute of Molecular Genetics of the Czech Academy of Sciences ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD                 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga E MTAB 8800:WKM 5 EaD s WKM 5 EaD s Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. Experimental Factor: stimulus:kit ligand RNA-Seq TRANSCRIPTOMIC Inverse rRNA SINGLE ILLUMINA NextSeq 500   ERP120057 NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 9_WKM_5_EaD.fastq.gz fastq 3602342027.0 47707938.0 E MTAB 8800:WKM 5 EaD 0:75.51 1:0 A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286 75 0     717278291 1084375347 1027250408 773351695 86286 ERX3938949 ERS4329526 ERA2383450 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 1 0.96461   0.20281   0.85303   0.74553   75   B   usable mapping rate illumina nextseq full_length rrna_depletion smarter bulk bulk bulk   Czech Republic 2021-12-31 Adult Adult Multi-tissue Multi-system
11226 11226 ERR10368639 ERX9900562 ERS13563108 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X9 SAMEA111469072 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469072|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X9|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X9                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X9 p 16261X9 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:snrnp70 / RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R1_001.fastq.gz 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R2_001.fastq.gz fastq fastq 2686590240.0 26339120.0 E MTAB 12301:16261X9 190815 A00421 0101 BHFL23DRXX S2 L001 R 0:51 1:51 A:694597606;C:635153638;G:628248232;T:728333026;N:257738 51 51     694597606 635153638 628248232 728333026 257738 ERX9900562 ERS13563108 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94614 0.94723 0.1538 0.15109 0.70398 0.70352 0.48123 0.48168 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11227 11227 ERR10368638 ERX9900561 ERS13563107 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X8 SAMEA111469071 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469071|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X8|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X8                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X8 p 16261X8 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:snrnp70 / RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R1_001.fastq.gz 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R2_001.fastq.gz fastq fastq 15003930006.0 147097353.0 E MTAB 12301:16261X8 190815 A00421 0101 BHFL23DRXX S4 L001 R 0:51 1:51 A:3882939949;C:3570150556;G:3520942177;T:4028462946;N:1434378 51 51     3882939949 3570150556 3520942177 4028462946 1434378 ERX9900561 ERS13563107 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94373 0.94762 0.17954 0.17832 0.70299 0.70207 0.48822 0.48842 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11228 11228 ERR10368637 ERX9900560 ERS13563106 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X7 SAMEA111469070 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469070|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X7|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X7                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X7 p 16261X7 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:snrnp70 / RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R1_001.fastq.gz 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R2_001.fastq.gz fastq fastq 3806643060.0 37320030.0 E MTAB 12301:16261X7 190815 A00421 0101 BHFL23DRXX S6 L001 R 0:51 1:51 A:971582421;C:919313664;G:905728446;T:1009653865;N:364664 51 51     971582421 919313664 905728446 1009653865 364664 ERX9900560 ERS13563106 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94035 0.94356 0.1661 0.16393 0.70136 0.70082 0.48294 0.48049 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11229 11229 ERR10368636 ERX9900559 ERS13563105 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X6 SAMEA111469069 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469069|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X6|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X6                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X6 p 16261X6 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:+/cyt hSNRNP70 RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R1_001.fastq.gz 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R2_001.fastq.gz fastq fastq 2875874598.0 28194849.0 E MTAB 12301:16261X6 190815 A00421 0101 BHFL23DRXX S7 L001 R 0:51 1:51 A:745870043;C:683782229;G:673037324;T:772909720;N:275282 51 51     745870043 683782229 673037324 772909720 275282 ERX9900559 ERS13563105 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.9435 0.94737 0.16987 0.16888 0.6983 0.69826 0.47122 0.47409 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11230 11230 ERR10368635 ERX9900558 ERS13563104 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X5 SAMEA111469068 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469068|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X5|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X5                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X5 p 16261X5 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:+/cyt hSNRNP70 RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R1_001.fastq.gz 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R2_001.fastq.gz fastq fastq 2656716072.0 26046236.0 E MTAB 12301:16261X5 190815 A00421 0101 BHFL23DRXX S8 L001 R 0:51 1:51 A:693979046;C:627484571;G:617505105;T:717493108;N:254242 51 51     693979046 627484571 617505105 717493108 254242 ERX9900558 ERS13563104 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94387 0.94796 0.16299 0.16183 0.69556 0.69581 0.46842 0.47334 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11231 11231 ERR10368634 ERX9900557 ERS13563103 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X4 SAMEA111469067 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469067|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X4|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X4                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X4 p 16261X4 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:+/cyt hSNRNP70 RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R1_001.fastq.gz 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R2_001.fastq.gz fastq fastq 2693177298.0 26403699.0 E MTAB 12301:16261X4 190815 A00421 0101 BHFL23DRXX S9 L001 R 0:51 1:51 A:698547378;C:640687214;G:628869192;T:724816757;N:256757 51 51     698547378 640687214 628869192 724816757 256757 ERX9900557 ERS13563103 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94101 0.94526 0.17344 0.17201 0.68619 0.68513 0.47366 0.4702 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11232 11232 ERR10368633 ERX9900556 ERS13563102 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X3 SAMEA111469066 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469066|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X3|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X3                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X3 p 16261X3 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py|options: dnus 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R1_001.fastq.gz 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R2_001.fastq.gz fastq fastq 3104796462.0 60878362.0 E MTAB 12301:16261X3 190815 A00421 0101 BHFL23DRXX S10 L001 R 0:51 A:803595677;C:737898133;G:731641815;T:831364716;N:296121 51       803595677 737898133 731641815 831364716 296121 ERX9900556 ERS13563102 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 1 0.94361   0.16161   0.69822   0.4647   51   B   usable mapping rate illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11233 11233 ERR10368632 ERX9900555 ERS13563101 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X2 SAMEA111469065 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469065|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X2|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X2                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X2 p 16261X2 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R1_001.fastq.gz 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R2_001.fastq.gz fastq fastq 2935625892.0 28780646.0 E MTAB 12301:16261X2 190815 A00421 0101 BHFL23DRXX S11 L001 R 0:51 1:51 A:759844700;C:699591057;G:694530268;T:781380766;N:279101 51 51     759844700 699591057 694530268 781380766 279101 ERX9900555 ERS13563101 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.93297 0.93744 0.16748 0.16566 0.69929 0.6996 0.4788 0.47875 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11234 11234 ERR10368631 ERX9900554 ERS13563100 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X12 SAMEA111469064 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469064|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X12|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X12                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X12 p 16261X12 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:cyt hSNRNP70/ RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R1_001.fastq.gz 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R2_001.fastq.gz fastq fastq 7451469240.0 73053620.0 E MTAB 12301:16261X12 190815 A00421 0101 BHFL23DRXX S3 L001 R 0:51 1:51 A:1950856364;C:1747213644;G:1718730947;T:2033957057;N:711228 51 51     1950856364 1747213644 1718730947 2033957057 711228 ERX9900554 ERS13563100 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.9372 0.94118 0.20267 0.19972 0.69794 0.69735 0.47505 0.4883 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11235 11235 ERR10368630 ERX9900553 ERS13563099 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X11 SAMEA111469063 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469063|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X11|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X11                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X11 p 16261X11 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:cyt hSNRNP70/ RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R1_001.fastq.gz 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R2_001.fastq.gz fastq fastq 2754589458.0 27005779.0 E MTAB 12301:16261X11 190815 A00421 0101 BHFL23DRXX S5 L001 R 0:51 1:51 A:715675810;C:652231961;G:640938288;T:745480460;N:262939 51 51     715675810 652231961 640938288 745480460 262939 ERX9900553 ERS13563099 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.93802 0.94247 0.17937 0.17728 0.70195 0.70067 0.48458 0.48364 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11236 11236 ERR10368629 ERX9900552 ERS13563098 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X10 SAMEA111469062 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469062|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X10|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X10                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X10 p 16261X10 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:cyt hSNRNP70/ RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R1_001.fastq.gz 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R2_001.fastq.gz fastq fastq 2319764682.0 22742791.0 E MTAB 12301:16261X10 190815 A00421 0101 BHFL23DRXX S1 L001 R 0:51 1:51 A:596937200;C:555502273;G:546190804;T:620912915;N:221490 51 51     596937200 555502273 546190804 620912915 221490 ERX9900552 ERS13563098 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94034 0.94451 0.1621 0.16043 0.69406 0.6928 0.4936 0.49757 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11237 11237 ERR10368628 ERX9900551 ERS13563097 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X1 SAMEA111469061 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469061|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X1|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X1                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X1 p 16261X1 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R1_001.fastq.gz 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R2_001.fastq.gz fastq fastq 2992675512.0 29339956.0 E MTAB 12301:16261X1 190815 A00421 0101 BHFL23DRXX S12 L001 R 0:51 1:51 A:768607745;C:718646844;G:713246748;T:791888447;N:285728 51 51     768607745 718646844 713246748 791888447 285728 ERX9900551 ERS13563097 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94414 0.94881 0.16725 0.16648 0.68909 0.68923 0.47873 0.48244 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11815 11815 ERR11799086 ERX11197445 ERS16222830 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 4 SAMEA114237385 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237385|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 4|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 4|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 4 p Sample 4 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz fastq fastq 19305011730.0 95569365.0 E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R 0:101 1:101 A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044 101 101     6768262250 3044091042 2847188942 6645295452 174044 ERX11197445 ERS16222830 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.57007 0.5231 0.45597 0.40582 0.91579 0.91674 0.58257 0.5625 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11816 11816 ERR11799088 ERX11197447 ERS16222832 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 6 SAMEA114237387 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237387|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 6|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 6|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 6 p Sample 6 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R2.fq.gz so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R1.fq.gz fastq fastq 21028230098.0 104100149.0 E MTAB 13228:so zf94 VW6 MDMF8 CD45hi mhc2dab MACA S60 R 0:101 1:101 A:6738894716;C:4007335499;G:3664578692;T:6617229148;N:192043 101 101     6738894716 4007335499 3664578692 6617229148 192043 ERX11197447 ERS16222832 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.69217 0.69414 0.45934 0.4539 0.86423 0.86344 0.64485 0.62976 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11817 11817 ERR11799085 ERX11197444 ERS16222829 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 3 SAMEA114237384 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237384|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 3|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 3|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 3 p Sample 3 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R1.fq.gz so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R2.fq.gz fastq fastq 20720724286.0 102577843.0 E MTAB 13228:so zf94 VW3 MDMG1 CD45lo mhc2dab MGA S57 R 0:101 1:101 A:7221245295;C:3305546836;G:3154595537;T:7039147315;N:189303 101 101     7221245295 3305546836 3154595537 7039147315 189303 ERX11197444 ERS16222829 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.6027 0.56103 0.46397 0.41738 0.90536 0.90473 0.59858 0.59246 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11818 11818 ERR11799087 ERX11197446 ERS16222831 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 5 SAMEA114237386 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237386|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 5|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 5|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 5 p Sample 5 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R2.fq.gz so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R1.fq.gz fastq fastq 20557799368.0 101771284.0 E MTAB 13228:so zf94 VW5 MDMF2 CD45hi mhc2dab MACA S59 R 0:101 1:101 A:5872430236;C:4635392917;G:4244261404;T:5805533335;N:181476 101 101     5872430236 4635392917 4244261404 5805533335 181476 ERX11197446 ERS16222831 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.48524 0.49426 0.30765 0.31318 0.87008 0.86918 0.60597 0.58678 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11819 11819 ERR11799083 ERX11197442 ERS16222827 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 1 SAMEA114237382 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237382|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 1|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 1 p Sample 1 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R2.fq.gz so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R1.fq.gz fastq fastq 24592452226.0 121744813.0 E MTAB 13228:so zf94 VW1 P2Y12 CD45lo MGA S55 R 0:101 1:101 A:6964719283;C:5587681189;G:5075783189;T:6964040906;N:227659 101 101     6964719283 5587681189 5075783189 6964040906 227659 ERX11197442 ERS16222827 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.82038 0.82668 0.39096 0.39605 0.82532 0.82446 0.63514 0.57014 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11820 11820 ERR11799084 ERX11197443 ERS16222828 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 2 SAMEA114237383 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237383|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 2|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 2|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 2 p Sample 2 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R2.fq.gz so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R1.fq.gz fastq fastq 23692841994.0 117291297.0 E MTAB 13228:so zf94 VW2 P2Y12 CD45lo MGA S56 R 0:101 1:101 A:6997658831;C:5103576511;G:4615471075;T:6975924499;N:211078 101 101     6997658831 5103576511 4615471075 6975924499 211078 ERX11197443 ERS16222828 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.78961 0.79279 0.39456 0.39476 0.8227 0.82309 0.62072 0.61776 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
15394 15394 ERR12724517 ERX12099016 ERS18400121 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 WT 2 E MTAB 13886:Foxg1 WT 2   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 WT 2 p Foxg1 WT 2 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X14_200629_A00421_0211_BHN23CDRXX_S26_L001_R1_001.fastq.gz 18067X14_200629_A00421_0211_BHN23CDRXX_S26_L001_R2_001.fastq.gz fastq fastq 4054926360.0 39754180.0 E MTAB 13886:18067X14 200629 A00421 0211 BHN23CDRXX S26 L001 R 0:51 1:51 A:1027112898;C:978274968;G:992295226;T:1057002684;N:240584 51 51     1027112898 978274968 992295226 1057002684 240584 ERX12099016 ERS18400121 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15395 15395 ERR12724511 ERX12099010 ERS18400115 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 9 E MTAB 13886:Foxg1 het 9   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 9 p Foxg1 het 9 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X11_200629_A00421_0211_BHN23CDRXX_S18_L001_R1_001.fastq.gz 18067X11_200629_A00421_0211_BHN23CDRXX_S18_L001_R2_001.fastq.gz fastq fastq 2866917570.0 28107035.0 E MTAB 13886:18067X11 200629 A00421 0211 BHN23CDRXX S18 L001 R 0:51 1:51 A:725353172;C:688761995;G:699694713;T:752936948;N:170742 51 51     725353172 688761995 699694713 752936948 170742 ERX12099010 ERS18400115 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15396 15396 ERR12724513 ERX12099012 ERS18400117 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 null 2 E MTAB 13886:Foxg1 null 2   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 null 2 p Foxg1 null 2 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X2_200629_A00421_0211_BHN23CDRXX_S27_L001_R1_001.fastq.gz 18067X2_200629_A00421_0211_BHN23CDRXX_S27_L001_R2_001.fastq.gz fastq fastq 2908778880.0 28517440.0 E MTAB 13886:18067X2 200629 A00421 0211 BHN23CDRXX S27 L001 R 0:51 1:51 A:734785178;C:700849624;G:712519278;T:760452796;N:172004 51 51     734785178 700849624 712519278 760452796 172004 ERX12099012 ERS18400117 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15397 15397 ERR12724507 ERX12099006 ERS18400111 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 5 E MTAB 13886:Foxg1 het 5   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 5 p Foxg1 het 5 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X7_200629_A00421_0211_BHN23CDRXX_S19_L001_R1_001.fastq.gz 18067X7_200629_A00421_0211_BHN23CDRXX_S19_L001_R2_001.fastq.gz fastq fastq 3111366282.0 30503591.0 E MTAB 13886:18067X7 200629 A00421 0211 BHN23CDRXX S19 L001 R 0:51 1:51 A:780094412;C:754603273;G:768441715;T:808041650;N:185232 51 51     780094412 754603273 768441715 808041650 185232 ERX12099006 ERS18400111 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15398 15398 ERR12724519 ERX12099018 ERS18400123 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 WT 6 E MTAB 13886:Foxg1 WT 6   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 WT 6 p Foxg1 WT 6 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X16_200629_A00421_0211_BHN23CDRXX_S22_L001_R1_001.fastq.gz 18067X16_200629_A00421_0211_BHN23CDRXX_S22_L001_R2_001.fastq.gz fastq fastq 3030554130.0 29711315.0 E MTAB 13886:18067X16 200629 A00421 0211 BHN23CDRXX S22 L001 R 0:51 1:51 A:770513445;C:725582256;G:737052763;T:797224111;N:181555 51 51     770513445 725582256 737052763 797224111 181555 ERX12099018 ERS18400123 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15399 15399 ERR12724510 ERX12099009 ERS18400114 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 8 E MTAB 13886:Foxg1 het 8   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 8 p Foxg1 het 8 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X10_200629_A00421_0211_BHN23CDRXX_S13_L001_R1_001.fastq.gz 18067X10_200629_A00421_0211_BHN23CDRXX_S13_L001_R2_001.fastq.gz fastq fastq 3601017894.0 35304097.0 E MTAB 13886:18067X10 200629 A00421 0211 BHN23CDRXX S13 L001 R 0:51 1:51 A:903986531;C:871550198;G:885398218;T:939870481;N:212466 51 51     903986531 871550198 885398218 939870481 212466 ERX12099009 ERS18400114 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15400 15400 ERR12724516 ERX12099015 ERS18400120 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 WT 1 E MTAB 13886:Foxg1 WT 1   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 WT 1 p Foxg1 WT 1 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X13_200629_A00421_0211_BHN23CDRXX_S14_L001_R1_001.fastq.gz 18067X13_200629_A00421_0211_BHN23CDRXX_S14_L001_R2_001.fastq.gz fastq fastq 4252867662.0 41694781.0 E MTAB 13886:18067X13 200629 A00421 0211 BHN23CDRXX S14 L001 R 0:51 1:51 A:1069523245;C:1031533375;G:1047047746;T:1104513602;N:249694 51 51     1069523245 1031533375 1047047746 1104513602 249694 ERX12099015 ERS18400120 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15401 15401 ERR12724505 ERX12099004 ERS18400109 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 2 E MTAB 13886:Foxg1 het 2   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 2 p Foxg1 het 2 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X5_200629_A00421_0211_BHN23CDRXX_S21_L001_R1_001.fastq.gz 18067X5_200629_A00421_0211_BHN23CDRXX_S21_L001_R2_001.fastq.gz fastq fastq 3490870236.0 34224218.0 E MTAB 13886:18067X5 200629 A00421 0211 BHN23CDRXX S21 L001 R 0:51 1:51 A:868722737;C:853509703;G:868564192;T:899868487;N:205117 51 51     868722737 853509703 868564192 899868487 205117 ERX12099004 ERS18400109 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15402 15402 ERR12724509 ERX12099008 ERS18400113 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 7 E MTAB 13886:Foxg1 het 7   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 7 p Foxg1 het 7 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X9_200629_A00421_0211_BHN23CDRXX_S15_L001_R1_001.fastq.gz 18067X9_200629_A00421_0211_BHN23CDRXX_S15_L001_R2_001.fastq.gz fastq fastq 3288698484.0 32242142.0 E MTAB 13886:18067X9 200629 A00421 0211 BHN23CDRXX S15 L001 R 0:51 1:51 A:849623075;C:775307492;G:786016403;T:877557952;N:193562 51 51     849623075 775307492 786016403 877557952 193562 ERX12099008 ERS18400113 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15403 15403 ERR12724512 ERX12099011 ERS18400116 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 null 1 E MTAB 13886:Foxg1 null 1   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 null 1 p Foxg1 null 1 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X1_200629_A00421_0211_BHN23CDRXX_S28_L001_R1_001.fastq.gz 18067X1_200629_A00421_0211_BHN23CDRXX_S28_L001_R2_001.fastq.gz fastq fastq 3735665544.0 36624172.0 E MTAB 13886:18067X1 200629 A00421 0211 BHN23CDRXX S28 L001 R 0:51 1:51 A:930463361;C:914183345;G:929494372;T:961303244;N:221222 51 51     930463361 914183345 929494372 961303244 221222 ERX12099011 ERS18400116 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15404 15404 ERR12724514 ERX12099013 ERS18400118 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 null 3 E MTAB 13886:Foxg1 null 3   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 null 3 p Foxg1 null 3 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X3_200629_A00421_0211_BHN23CDRXX_S25_L001_R1_001.fastq.gz 18067X3_200629_A00421_0211_BHN23CDRXX_S25_L001_R2_001.fastq.gz fastq fastq 3581623512.0 35113956.0 E MTAB 13886:18067X3 200629 A00421 0211 BHN23CDRXX S25 L001 R 0:51 1:51 A:901782474;C:866330420;G:882309046;T:930988392;N:213180 51 51     901782474 866330420 882309046 930988392 213180 ERX12099013 ERS18400118 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15405 15405 ERR12724504 ERX12099003 ERS18400108 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 13 E MTAB 13886:Foxg1 het 13   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 13 p Foxg1 het 13 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X12_200629_A00421_0211_BHN23CDRXX_S16_L001_R1_001.fastq.gz 18067X12_200629_A00421_0211_BHN23CDRXX_S16_L001_R2_001.fastq.gz fastq fastq 3198417570.0 31357035.0 E MTAB 13886:18067X12 200629 A00421 0211 BHN23CDRXX S16 L001 R 0:51 1:51 A:806440222;C:774073728;G:785492238;T:832222984;N:188398 51 51     806440222 774073728 785492238 832222984 188398 ERX12099003 ERS18400108 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15406 15406 ERR12724508 ERX12099007 ERS18400112 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 6 E MTAB 13886:Foxg1 het 6   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 6 p Foxg1 het 6 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X8_200629_A00421_0211_BHN23CDRXX_S17_L001_R1_001.fastq.gz 18067X8_200629_A00421_0211_BHN23CDRXX_S17_L001_R2_001.fastq.gz fastq fastq 2829840366.0 27743533.0 E MTAB 13886:18067X8 200629 A00421 0211 BHN23CDRXX S17 L001 R 0:51 1:51 A:712954704;C:683604864;G:696251651;T:736863084;N:166063 51 51     712954704 683604864 696251651 736863084 166063 ERX12099007 ERS18400112 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15407 15407 ERR12724506 ERX12099005 ERS18400110 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 3 E MTAB 13886:Foxg1 het 3   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 3 p Foxg1 het 3 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X6_200629_A00421_0211_BHN23CDRXX_S20_L001_R1_001.fastq.gz 18067X6_200629_A00421_0211_BHN23CDRXX_S20_L001_R2_001.fastq.gz fastq fastq 2947992168.0 28901884.0 E MTAB 13886:18067X6 200629 A00421 0211 BHN23CDRXX S20 L001 R 0:51 1:51 A:745555818;C:709342231;G:720902928;T:772016275;N:174916 51 51     745555818 709342231 720902928 772016275 174916 ERX12099005 ERS18400110 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15408 15408 ERR12724515 ERX12099014 ERS18400119 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 null 6 E MTAB 13886:Foxg1 null 6   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 null 6 p Foxg1 null 6 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X4_200629_A00421_0211_BHN23CDRXX_S23_L001_R1_001.fastq.gz 18067X4_200629_A00421_0211_BHN23CDRXX_S23_L001_R2_001.fastq.gz fastq fastq 3166535838.0 31044469.0 E MTAB 13886:18067X4 200629 A00421 0211 BHN23CDRXX S23 L001 R 0:51 1:51 A:781063082;C:780685132;G:798403519;T:806197923;N:186182 51 51     781063082 780685132 798403519 806197923 186182 ERX12099014 ERS18400119 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15409 15409 ERR12724518 ERX12099017 ERS18400122 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 WT 5 E MTAB 13886:Foxg1 WT 5   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 WT 5 p Foxg1 WT 5 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X15_200629_A00421_0211_BHN23CDRXX_S24_L001_R1_001.fastq.gz 18067X15_200629_A00421_0211_BHN23CDRXX_S24_L001_R2_001.fastq.gz fastq fastq 3253306932.0 31895166.0 E MTAB 13886:18067X15 200629 A00421 0211 BHN23CDRXX S24 L001 R 0:51 1:51 A:822636212;C:784647591;G:797221431;T:848609081;N:192617 51 51     822636212 784647591 797221431 848609081 192617 ERX12099017 ERS18400122 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures

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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");;