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196 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.platform = "ILLUMINA" and tissue_curation = "Lateral Line"

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  • Lateral Line · 196 ✖

experiment.platform 1

  • ILLUMINA · 196 ✖

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experiment.library_source 1

  • TRANSCRIPTOMIC · 196 ✖

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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
50723 50723 SRR8270602 SRX5087288 SRS4099391 SRP171998 PRJNA507898 Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration GSE123241 Transcriptome Analysis Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells zebrafish ear and lateral line hair cells regenerate from poorly characterized proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type fgf3 mutants and fgf3 siblings.   pubmed:30681411;pubmed:31488837   fgf3 mutant GSM3498554   source name:neuromast|age:5dpf|tissue:neuromast|genotype:fgf3 / |strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t screened for mutants fgf3 mutant Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell. neuromast   Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq   age:5dpf|tissue:neuromast|genotype:fgf3 / |strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t screened for mutants GSM3498554 GSM3498554: fgf3 mutant; Danio rerio; RNA Seq GSM3498554   1 Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq GEO Accession:GSM3498554 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP171998     possorted_genome_bam_fgf3_mut.bam 10X Genomics bam file 16974126576.0 171455824.0 GSM3498554 r1 0:99 A:5250835858;C:3266700009;G:3497115040;T:4840312852;N:119162817 99       5250835858 3266700009 3497115040 4840312852 119162817 SRX5087288 SRS4099391 SRA817952 GEO Stowers Institute 1 0.89941   0.21879   0.80805   0.48702   99   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2018-12-02 Larval Larval Lateral Line Sensory System
50724 50724 SRR8270601 SRX5087287 SRS4099390 SRP171998 PRJNA507898 Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration GSE123241 Transcriptome Analysis Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells zebrafish ear and lateral line hair cells regenerate from poorly characterized proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type fgf3 mutants and fgf3 siblings.   pubmed:30681411;pubmed:31488837   fgf3 sibling GSM3498553   source name:neuromast|age:5dpf|tissue:neuromast|genotype:fgf3+/ |strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t fgf3 sibling Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell. neuromast   Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq   age:5dpf|tissue:neuromast|genotype:fgf3+/ |strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t GSM3498553 GSM3498553: fgf3 sibling; Danio rerio; RNA Seq GSM3498553   1 Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq GEO Accession:GSM3498553 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP171998     possorted_genome_bam_fgf3_sib.bam 10X Genomics bam file 15833733894.0 159936706.0 GSM3498553 r1 0:99 A:4876827108;C:3036857735;G:3248946665;T:4560644612;N:110457774 99       4876827108 3036857735 3248946665 4560644612 110457774 SRX5087287 SRS4099390 SRA817952 GEO Stowers Institute 1 0.89735   0.21699   0.80409   0.4894   99   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2018-12-02 Larval Larval Lateral Line Sensory System
50725 50725 SRR8270600 SRX5087286 SRS4099389 SRP171998 PRJNA507898 Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration GSE123241 Transcriptome Analysis Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells zebrafish ear and lateral line hair cells regenerate from poorly characterized proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type fgf3 mutants and fgf3 siblings.   pubmed:30681411;pubmed:31488837   WT GSM3498552   source name:neuromast|age:5dpf|tissue:neuromast|genotype:WT|strain:ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t WT Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell. neuromast   Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq   age:5dpf|tissue:neuromast|genotype:WT|strain:ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t GSM3498552 GSM3498552: WT; Danio rerio; RNA Seq GSM3498552   1 Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq GEO Accession:GSM3498552 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP171998     possorted_genome_bam_WT.bam 10X Genomics bam file 32918660478.0 332511722.0 GSM3498552 r1 0:99 A:10031241232;C:6365493396;G:6804558002;T:9674542542;N:42825306 99       10031241232 6365493396 6804558002 9674542542 42825306 SRX5087286 SRS4099389 SRA817952 GEO Stowers Institute 1 0.90685   0.26503   0.79368   0.47639   99   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2018-12-02 Larval Larval Lateral Line Sensory System
56093 56093 SRR10887617 SRX7556598 SRS5993979 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TGCGGC: hair cells wt 4H11 GSM4271797   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TGCGGC: hair cells wt 4H11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271797 GSM4271797: TGCGGC: hair cells wt 4H11; Danio rerio; RNA Seq GSM4271797   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271797 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TGCGGC_r1.fq.gz GEO_TGCGGC_r2.fq.gz fastq fastq 43663620.0 661570.0 GSM4271797 r1 0:16 1:50 A:10980262;C:9600102;G:10988621;T:12083118;N:11517 16 50     10980262 9600102 10988621 12083118 11517 SRX7556598 SRS5993979 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.89859 0.0 0.07802 1.0 0.97682   0.4968 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56094 56094 SRR10887616 SRX7556597 SRS5993978 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCGGCG: hair cells wt 4H10 GSM4271796   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCGGCG: hair cells wt 4H10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271796 GSM4271796: TCGGCG: hair cells wt 4H10; Danio rerio; RNA Seq GSM4271796   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCGGCG_r1.fq.gz GEO_TCGGCG_r2.fq.gz fastq fastq 22768350.0 344975.0 GSM4271796 r1 0:16 1:50 A:5596078;C:4886377;G:5930717;T:6350111;N:5067 16 50     5596078 4886377 5930717 6350111 5067 SRX7556597 SRS5993978 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88535 0.0 0.08707 1.0 0.98494   0.4351 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56095 56095 SRR10887615 SRX7556596 SRS5993982 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCCCCG: hair cells wt 4H9 GSM4271795   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCCCCG: hair cells wt 4H9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271795 GSM4271795: TCCCCG: hair cells wt 4H9; Danio rerio; RNA Seq GSM4271795   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCCCCG_r1.fq.gz GEO_TCCCCG_r2.fq.gz fastq fastq 38242578.0 579433.0 GSM4271795 r1 0:16 1:50 A:9595312;C:9433451;G:8997891;T:10207672;N:8252 16 50     9595312 9433451 8997891 10207672 8252 SRX7556596 SRS5993982 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81703 0.0 0.06164 1.0 0.97768   0.49143 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56096 56096 SRR10887614 SRX7556595 SRS5993977 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GTCGGC: hair cells wt 4H8 GSM4271794   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GTCGGC: hair cells wt 4H8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271794 GSM4271794: GTCGGC: hair cells wt 4H8; Danio rerio; RNA Seq GSM4271794   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271794 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GTCGGC_r2.fq.gz GEO_GTCGGC_r1.fq.gz fastq fastq 24562824.0 372164.0 GSM4271794 r1 0:16 1:50 A:6106780;C:5478045;G:6286868;T:6684497;N:6634 16 50     6106780 5478045 6286868 6684497 6634 SRX7556595 SRS5993977 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86176 0.0 0.07352 1.0 0.98052   0.45168 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56097 56097 SRR10887613 SRX7556594 SRS5993976 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGTGCG: hair cells wt 4H7 GSM4271793   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGTGCG: hair cells wt 4H7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271793 GSM4271793: GGTGCG: hair cells wt 4H7; Danio rerio; RNA Seq GSM4271793   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271793 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGTGCG_r1.fq.gz GEO_GGTGCG_r2.fq.gz fastq fastq 24573120.0 372320.0 GSM4271793 r1 0:16 1:50 A:6100442;C:5201156;G:6470564;T:6794081;N:6877 16 50     6100442 5201156 6470564 6794081 6877 SRX7556594 SRS5993976 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.84609 0.0 0.07426 1.0 0.98549   0.38014 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56098 56098 SRR10887612 SRX7556593 SRS5993981 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCGGGA: hair cells wt 4G11 GSM4271792   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCGGGA: hair cells wt 4G11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271792 GSM4271792: GCGGGA: hair cells wt 4G11; Danio rerio; RNA Seq GSM4271792   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271792 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCGGGA_r1.fq.gz GEO_GCGGGA_r2.fq.gz fastq fastq 27407886.0 415271.0 GSM4271792 r1 0:16 1:50 A:7308875;C:5649646;G:7245666;T:7196334;N:7365 16 50     7308875 5649646 7245666 7196334 7365 SRX7556593 SRS5993981 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86238 0.0 0.07458 1.0 0.98571   0.47913 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56099 56099 SRR10887611 SRX7556592 SRS5993974 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCGCGT: hair cells wt 4G10 GSM4271791   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCGCGT: hair cells wt 4G10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271791 GSM4271791: GCGCGT: hair cells wt 4G10; Danio rerio; RNA Seq GSM4271791   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271791 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCGCGT_r1.fq.gz GEO_GCGCGT_r2.fq.gz fastq fastq 20750466.0 314401.0 GSM4271791 r1 0:16 1:50 A:5141353;C:4540611;G:5281606;T:5781160;N:5736 16 50     5141353 4540611 5281606 5781160 5736 SRX7556592 SRS5993974 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88471 0.0 0.07169 1.0 0.98707   0.42399 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56100 56100 SRR10887610 SRX7556591 SRS5993973 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCGACG: hair cells wt 4G9 GSM4271790   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCGACG: hair cells wt 4G9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271790 GSM4271790: GCGACG: hair cells wt 4G9; Danio rerio; RNA Seq GSM4271790   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCGACG_r1.fq.gz GEO_GCGACG_r2.fq.gz fastq fastq 19658100.0 297850.0 GSM4271790 r1 0:16 1:50 A:5205744;C:4275466;G:5026996;T:5144761;N:5133 16 50     5205744 4275466 5026996 5144761 5133 SRX7556591 SRS5993973 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.89191 0.0 0.06686 1.0 0.98131   0.54948 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56101 56101 SRR10887609 SRX7556590 SRS5993975 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCCGGT: hair cells wt 4G8 GSM4271789   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCCGGT: hair cells wt 4G8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271789 GSM4271789: GCCGGT: hair cells wt 4G8; Danio rerio; RNA Seq GSM4271789   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271789 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCCGGT_r1.fq.gz GEO_GCCGGT_r2.fq.gz fastq fastq 34655676.0 525086.0 GSM4271789 r1 0:16 1:50 A:8563248;C:7767967;G:8892276;T:9422886;N:9299 16 50     8563248 7767967 8892276 9422886 9299 SRX7556590 SRS5993975 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.85312 0.0 0.06695 1.0 0.98524   0.39088 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56102 56102 SRR10887608 SRX7556589 SRS5993980 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCCCGA: hair cells wt 4G7 GSM4271788   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCCCGA: hair cells wt 4G7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271788 GSM4271788: GCCCGA: hair cells wt 4G7; Danio rerio; RNA Seq GSM4271788   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271788 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCCCGA_r1.fq.gz GEO_GCCCGA_r2.fq.gz fastq fastq 47296194.0 716609.0 GSM4271788 r1 0:16 1:50 A:12506634;C:11308000;G:11147016;T:12323583;N:10961 16 50     12506634 11308000 11147016 12323583 10961 SRX7556589 SRS5993980 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.75974 0.0 0.07461 1.0 0.98143   0.44424 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56103 56103 SRR10887607 SRX7556588 SRS5993972 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGGTCC: hair cells wt 4F12 GSM4271787   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGGTCC: hair cells wt 4F12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271787 GSM4271787: CGGTCC: hair cells wt 4F12; Danio rerio; RNA Seq GSM4271787   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271787 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGGTCC_r1.fq.gz GEO_CGGTCC_r2.fq.gz fastq fastq 25047000.0 379500.0 GSM4271787 r1 0:16 1:50 A:5998231;C:6033916;G:6166856;T:6841133;N:6864 16 50     5998231 6033916 6166856 6841133 6864 SRX7556588 SRS5993972 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86579 0.0 0.06304 1.0 0.98557   0.40593 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56104 56104 SRR10887606 SRX7556587 SRS5993971 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGGGAG: hair cells wt 4F11 GSM4271786   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGGGAG: hair cells wt 4F11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271786 GSM4271786: CGGGAG: hair cells wt 4F11; Danio rerio; RNA Seq GSM4271786   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271786 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGGGAG_r1.fq.gz GEO_CGGGAG_r2.fq.gz fastq fastq 17233986.0 261121.0 GSM4271786 r1 0:16 1:50 A:4479383;C:3511799;G:4707128;T:4530531;N:5145 16 50     4479383 3511799 4707128 4530531 5145 SRX7556587 SRS5993971 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.89442 0.0 0.07953 1.0 0.98524   0.47235 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56105 56105 SRR10887605 SRX7556586 SRS5993987 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGGCAC: hair cells wt 4F10 GSM4271785   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGGCAC: hair cells wt 4F10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271785 GSM4271785: CGGCAC: hair cells wt 4F10; Danio rerio; RNA Seq GSM4271785   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271785 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGGCAC_r1.fq.gz GEO_CGGCAC_r2.fq.gz fastq fastq 30505200.0 462200.0 GSM4271785 r1 0:16 1:50 A:8102580;C:6867077;G:7305104;T:8221444;N:8995 16 50     8102580 6867077 7305104 8221444 8995 SRX7556586 SRS5993987 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.89338 0.0 0.08357 1.0 0.98557   0.50949 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56106 56106 SRR10887604 SRX7556585 SRS5993968 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGCTCG: hair cells wt 4F9 GSM4271784   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGCTCG: hair cells wt 4F9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271784 GSM4271784: CGCTCG: hair cells wt 4F9; Danio rerio; RNA Seq GSM4271784   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271784 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGCTCG_r2.fq.gz GEO_CGCTCG_r1.fq.gz fastq fastq 52351398.0 793203.0 GSM4271784 r1 0:16 1:50 A:12807706;C:12020314;G:13385072;T:14123256;N:15050 16 50     12807706 12020314 13385072 14123256 15050 SRX7556585 SRS5993968 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.57439 0.0 0.06392 1.0 0.98253   0.42209 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56107 56107 SRR10887603 SRX7556584 SRS5993969 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGCGAC: hair cells wt 4F8 GSM4271783   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGCGAC: hair cells wt 4F8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271783 GSM4271783: CGCGAC: hair cells wt 4F8; Danio rerio; RNA Seq GSM4271783   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271783 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGCGAC_r1.fq.gz GEO_CGCGAC_r2.fq.gz fastq fastq 23345586.0 353721.0 GSM4271783 r1 0:16 1:50 A:6171925;C:5383523;G:5555672;T:6227469;N:6997 16 50     6171925 5383523 5555672 6227469 6997 SRX7556584 SRS5993969 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.8601 0.0 0.10116 1.0 0.98419   0.4521 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56108 56108 SRR10887602 SRX7556583 SRS5993967 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGCCAG: hair cells wt 4F7 GSM4271782   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGCCAG: hair cells wt 4F7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271782 GSM4271782: CGCCAG: hair cells wt 4F7; Danio rerio; RNA Seq GSM4271782   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271782 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGCCAG_r1.fq.gz GEO_CGCCAG_r2.fq.gz fastq fastq 14317578.0 216933.0 GSM4271782 r1 0:16 1:50 A:3909348;C:3253582;G:3411025;T:3739224;N:4399 16 50     3909348 3253582 3411025 3739224 4399 SRX7556583 SRS5993967 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.79255 0.0 0.14794 1.0 0.98644   0.60725 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56109 56109 SRR10887601 SRX7556582 SRS5993986 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CCAGGG: hair cells wt 4E12 GSM4271781   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CCAGGG: hair cells wt 4E12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271781 GSM4271781: CCAGGG: hair cells wt 4E12; Danio rerio; RNA Seq GSM4271781   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271781 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CCAGGG_r1.fq.gz GEO_CCAGGG_r2.fq.gz fastq fastq 24273084.0 367774.0 GSM4271781 r1 0:16 1:50 A:6469335;C:5140316;G:6075899;T:6580531;N:7003 16 50     6469335 5140316 6075899 6580531 7003 SRX7556582 SRS5993986 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86792 0.0 0.13118 1.0 0.98466   0.51743 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56110 56110 SRR10887600 SRX7556581 SRS5993966 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CAGGCC: hair cells wt 4E11 GSM4271780   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CAGGCC: hair cells wt 4E11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271780 GSM4271780: CAGGCC: hair cells wt 4E11; Danio rerio; RNA Seq GSM4271780   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271780 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CAGGCC_r2.fq.gz GEO_CAGGCC_r1.fq.gz fastq fastq 21957210.0 332685.0 GSM4271780 r1 0:16 1:50 A:5733552;C:5210288;G:5238165;T:5768948;N:6257 16 50     5733552 5210288 5238165 5768948 6257 SRX7556581 SRS5993966 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.82741 0.0 0.0895 1.0 0.9862   0.50397 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56111 56111 SRR10887599 SRX7556580 SRS5993970 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CACGCG: hair cells wt 4E10 GSM4271779   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CACGCG: hair cells wt 4E10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271779 GSM4271779: CACGCG: hair cells wt 4E10; Danio rerio; RNA Seq GSM4271779   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271779 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CACGCG_r1.fq.gz GEO_CACGCG_r2.fq.gz fastq fastq 25959582.0 393327.0 GSM4271779 r1 0:16 1:50 A:6981800;C:5837017;G:6108203;T:7025734;N:6828 16 50     6981800 5837017 6108203 7025734 6828 SRX7556580 SRS5993970 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86201 0.0 0.10766 1.0 0.98464   0.46435 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56112 56112 SRR10887598 SRX7556579 SRS5993965 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGGGCG: hair cells wt 4E9 GSM4271778   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGGGCG: hair cells wt 4E9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271778 GSM4271778: AGGGCG: hair cells wt 4E9; Danio rerio; RNA Seq GSM4271778   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271778 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGGGCG_r1.fq.gz GEO_AGGGCG_r2.fq.gz fastq fastq 22538274.0 341489.0 GSM4271778 r1 0:16 1:50 A:6077196;C:4338921;G:5951815;T:6165292;N:5050 16 50     6077196 4338921 5951815 6165292 5050 SRX7556579 SRS5993965 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.8557 0.0 0.1692 1.0 0.98042   0.55115 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56113 56113 SRR10887597 SRX7556578 SRS5993984 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGCGCC: hair cells wt 4E8 GSM4271777   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGCGCC: hair cells wt 4E8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271777 GSM4271777: AGCGCC: hair cells wt 4E8; Danio rerio; RNA Seq GSM4271777   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271777 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGCGCC_r1.fq.gz GEO_AGCGCC_r2.fq.gz fastq fastq 16579134.0 251199.0 GSM4271777 r1 0:16 1:50 A:4407189;C:3879034;G:3989040;T:4299921;N:3950 16 50     4407189 3879034 3989040 4299921 3950 SRX7556578 SRS5993984 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81806 0.0 0.06974 1.0 0.9847   0.47148 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56114 56114 SRR10887596 SRX7556577 SRS5993985 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACGGCC: hair cells wt 4E7 GSM4271776   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACGGCC: hair cells wt 4E7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271776 GSM4271776: ACGGCC: hair cells wt 4E7; Danio rerio; RNA Seq GSM4271776   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271776 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACGGCC_r1.fq.gz GEO_ACGGCC_r2.fq.gz fastq fastq 118857420.0 1800870.0 GSM4271776 r1 0:16 1:50 A:29791771;C:29519453;G:31033819;T:28481312;N:31065 16 50     29791771 29519453 31033819 28481312 31065 SRX7556577 SRS5993985 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.72883 0.0 0.23389 1.0 0.97792   0.5079 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56115 56115 SRR10887595 SRX7556576 SRS5993962 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GATCGT: hair cells wt 4D12 GSM4271775   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GATCGT: hair cells wt 4D12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271775 GSM4271775: GATCGT: hair cells wt 4D12; Danio rerio; RNA Seq GSM4271775   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271775 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GATCGT_r1.fq.gz GEO_GATCGT_r2.fq.gz fastq fastq 33894102.0 513547.0 GSM4271775 r1 0:16 1:50 A:8954709;C:6672608;G:8290536;T:9966379;N:9870 16 50     8954709 6672608 8290536 9966379 9870 SRX7556576 SRS5993962 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88831 0.0 0.07983 1.0 0.98029   0.48458 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56116 56116 SRR10887594 SRX7556575 SRS5993964 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGATTG: hair cells wt 4D11 GSM4271774   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGATTG: hair cells wt 4D11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271774 GSM4271774: CGATTG: hair cells wt 4D11; Danio rerio; RNA Seq GSM4271774   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271774 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGATTG_r1.fq.gz GEO_CGATTG_r2.fq.gz fastq fastq 18082020.0 273970.0 GSM4271774 r1 0:16 1:50 A:4869073;C:3585379;G:4430790;T:5191055;N:5723 16 50     4869073 3585379 4430790 5191055 5723 SRX7556575 SRS5993964 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.84709 0.0 0.19188 1.0 0.98086   0.52053 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56117 56117 SRR10887593 SRX7556574 SRS5993960 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CATGGT: hair cells wt 4D10 GSM4271773   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CATGGT: hair cells wt 4D10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271773 GSM4271773: CATGGT: hair cells wt 4D10; Danio rerio; RNA Seq GSM4271773   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271773 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CATGGT_r1.fq.gz GEO_CATGGT_r2.fq.gz fastq fastq 22401654.0 339419.0 GSM4271773 r1 0:16 1:50 A:5861732;C:4558444;G:5514064;T:6461033;N:6381 16 50     5861732 4558444 5514064 6461033 6381 SRX7556574 SRS5993960 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.85022 0.0 0.07553 1.0 0.98433   0.43146 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56118 56118 SRR10887592 SRX7556573 SRS5993961 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CAAGCT: hair cells wt 4D9 GSM4271772   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CAAGCT: hair cells wt 4D9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271772 GSM4271772: CAAGCT: hair cells wt 4D9; Danio rerio; RNA Seq GSM4271772   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271772 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CAAGCT_r1.fq.gz GEO_CAAGCT_r2.fq.gz fastq fastq 21428154.0 324669.0 GSM4271772 r1 0:16 1:50 A:5942829;C:4731188;G:4990655;T:5756895;N:6587 16 50     5942829 4731188 4990655 5756895 6587 SRX7556573 SRS5993961 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.84948 0.0 0.11697 1.0 0.98482   0.49134 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56119 56119 SRR10887591 SRX7556572 SRS5993958 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACCGTA: hair cells wt 4D8 GSM4271771   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACCGTA: hair cells wt 4D8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271771 GSM4271771: ACCGTA: hair cells wt 4D8; Danio rerio; RNA Seq GSM4271771   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271771 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACCGTA_r1.fq.gz GEO_ACCGTA_r2.fq.gz fastq fastq 32023728.0 485208.0 GSM4271771 r1 0:16 1:50 A:8851322;C:7094664;G:7465921;T:8602598;N:9223 16 50     8851322 7094664 7465921 8602598 9223 SRX7556572 SRS5993958 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81584 0.0 0.07569 1.0 0.98701   0.43154 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56120 56120 SRR10887590 SRX7556571 SRS5993957 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TTTTCT: hair cells wt 4D7 GSM4271770   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TTTTCT: hair cells wt 4D7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271770 GSM4271770: TTTTCT: hair cells wt 4D7; Danio rerio; RNA Seq GSM4271770   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271770 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TTTTCT_r1.fq.gz GEO_TTTTCT_r2.fq.gz fastq fastq 30970962.0 469257.0 GSM4271770 r1 0:16 1:50 A:7685607;C:6225340;G:6659308;T:10392742;N:7965 16 50     7685607 6225340 6659308 10392742 7965 SRX7556571 SRS5993957 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.83325 0.0 0.10718 1.0 0.98157   0.49058 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56121 56121 SRR10887589 SRX7556570 SRS5993955 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TGTTAT: hair cells wt 4C12 GSM4271769   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TGTTAT: hair cells wt 4C12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271769 GSM4271769: TGTTAT: hair cells wt 4C12; Danio rerio; RNA Seq GSM4271769   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271769 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TGTTAT_r1.fq.gz GEO_TGTTAT_r2.fq.gz fastq fastq 27958458.0 423613.0 GSM4271769 r1 0:16 1:50 A:7253350;C:5460413;G:6559816;T:8677521;N:7358 16 50     7253350 5460413 6559816 8677521 7358 SRX7556570 SRS5993955 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.83012 0.0 0.08904 1.0 0.98675   0.37785 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56122 56122 SRR10887588 SRX7556569 SRS5993963 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TGATAA: hair cells wt 4C11 GSM4271768   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TGATAA: hair cells wt 4C11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271768 GSM4271768: TGATAA: hair cells wt 4C11; Danio rerio; RNA Seq GSM4271768   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271768 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TGATAA_r1.fq.gz GEO_TGATAA_r2.fq.gz fastq fastq 16311570.0 247145.0 GSM4271768 r1 0:16 1:50 A:4698682;C:3073287;G:3789253;T:4746028;N:4320 16 50     4698682 3073287 3789253 4746028 4320 SRX7556569 SRS5993963 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.83888 0.0 0.09183 1.0 0.98715   0.45564 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56123 56123 SRR10887587 SRX7556568 SRS5993959 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCTATA: hair cells wt 4C10 GSM4271767   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCTATA: hair cells wt 4C10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271767 GSM4271767: TCTATA: hair cells wt 4C10; Danio rerio; RNA Seq GSM4271767   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271767 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCTATA_r1.fq.gz GEO_TCTATA_r2.fq.gz fastq fastq 21750102.0 329547.0 GSM4271767 r1 0:16 1:50 A:6098788;C:4298102;G:4613696;T:6733786;N:5730 16 50     6098788 4298102 4613696 6733786 5730 SRX7556568 SRS5993959 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88556 0.0 0.09247 1.0 0.98632   0.51526 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56124 56124 SRR10887586 SRX7556567 SRS5993954 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCAATT: hair cells wt 4C9 GSM4271766   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCAATT: hair cells wt 4C9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271766 GSM4271766: TCAATT: hair cells wt 4C9; Danio rerio; RNA Seq GSM4271766   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271766 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCAATT_r1.fq.gz GEO_TCAATT_r2.fq.gz fastq fastq 23862894.0 361559.0 GSM4271766 r1 0:16 1:50 A:6588667;C:4897780;G:5179183;T:7191284;N:5980 16 50     6588667 4897780 5179183 7191284 5980 SRX7556567 SRS5993954 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86481 0.0 0.11034 1.0 0.98326   0.40522 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56125 56125 SRR10887585 SRX7556566 SRS5993956 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TATTCA: hair cells wt 4C8 GSM4271765   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TATTCA: hair cells wt 4C8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271765 GSM4271765: TATTCA: hair cells wt 4C8; Danio rerio; RNA Seq GSM4271765   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271765 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TATTCA_r1.fq.gz GEO_TATTCA_r2.fq.gz fastq fastq 17886990.0 271015.0 GSM4271765 r1 0:16 1:50 A:4891618;C:3686776;G:3988141;T:5315845;N:4610 16 50     4891618 3686776 3988141 5315845 4610 SRX7556566 SRS5993956 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81672 0.0 0.1005 1.0 0.98561   0.42678 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56126 56126 SRR10887584 SRX7556565 SRS5993952 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TATCTA: hair cells wt 4C7 GSM4271764   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TATCTA: hair cells wt 4C7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271764 GSM4271764: TATCTA: hair cells wt 4C7; Danio rerio; RNA Seq GSM4271764   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271764 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TATCTA_r1.fq.gz GEO_TATCTA_r2.fq.gz fastq fastq 67991880.0 1030180.0 GSM4271764 r1 0:16 1:50 A:18256048;C:14118538;G:16365381;T:19234623;N:17290 16 50     18256048 14118538 16365381 19234623 17290 SRX7556565 SRS5993952 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.74612 0.0 0.10089 1.0 0.97877   0.49534 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56127 56127 SRR10887583 SRX7556564 SRS5993953 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GTTATT: hair cells wt 4B12 GSM4271763   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GTTATT: hair cells wt 4B12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271763 GSM4271763: GTTATT: hair cells wt 4B12; Danio rerio; RNA Seq GSM4271763   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271763 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GTTATT_r1.fq.gz GEO_GTTATT_r2.fq.gz fastq fastq 33621720.0 509420.0 GSM4271763 r1 0:16 1:50 A:8782917;C:6333781;G:7803342;T:10694526;N:7154 16 50     8782917 6333781 7803342 10694526 7154 SRX7556564 SRS5993953 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.83277 0.0 0.09046 1.0 0.98208   0.42767 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56128 56128 SRR10887582 SRX7556563 SRS5993950 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GTAAAT: hair cells wt 4B11 GSM4271762   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GTAAAT: hair cells wt 4B11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271762 GSM4271762: GTAAAT: hair cells wt 4B11; Danio rerio; RNA Seq GSM4271762   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271762 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GTAAAT_r1.fq.gz GEO_GTAAAT_r2.fq.gz fastq fastq 32995116.0 499926.0 GSM4271762 r1 0:16 1:50 A:9697104;C:6185335;G:7695283;T:9409420;N:7974 16 50     9697104 6185335 7695283 9409420 7974 SRX7556563 SRS5993950 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86836 0.0 0.1074 1.0 0.98384   0.42561 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56129 56129 SRR10887581 SRX7556562 SRS5993949 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GAATTA: hair cells wt 4B10 GSM4271761   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GAATTA: hair cells wt 4B10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271761 GSM4271761: GAATTA: hair cells wt 4B10; Danio rerio; RNA Seq GSM4271761   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271761 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GAATTA_r1.fq.gz GEO_GAATTA_r2.fq.gz fastq fastq 33700524.0 510614.0 GSM4271761 r1 0:16 1:50 A:9951851;C:6205852;G:7868259;T:9667023;N:7539 16 50     9951851 6205852 7868259 9667023 7539 SRX7556562 SRS5993949 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86693 0.0 0.08211 1.0 0.9807   0.4477 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56130 56130 SRR10887580 SRX7556561 SRS5993951 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CTTATA: hair cells wt 4B9 GSM4271760   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CTTATA: hair cells wt 4B9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271760 GSM4271760: CTTATA: hair cells wt 4B9; Danio rerio; RNA Seq GSM4271760   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271760 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CTTATA_r2.fq.gz GEO_CTTATA_r1.fq.gz fastq fastq 18144654.0 274919.0 GSM4271760 r1 0:16 1:50 A:5154253;C:3585215;G:3991271;T:5409596;N:4319 16 50     5154253 3585215 3991271 5409596 4319 SRX7556561 SRS5993951 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81083 0.0 0.12691 1.0 0.97979   0.53705 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56131 56131 SRR10887579 SRX7556560 SRS5993947 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CTAATT: hair cells wt 4B8 GSM4271759   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CTAATT: hair cells wt 4B8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271759 GSM4271759: CTAATT: hair cells wt 4B8; Danio rerio; RNA Seq GSM4271759   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271759 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CTAATT_r1.fq.gz GEO_CTAATT_r2.fq.gz fastq fastq 21875304.0 331444.0 GSM4271759 r1 0:16 1:50 A:6178378;C:4411583;G:4735412;T:6545030;N:4901 16 50     6178378 4411583 4735412 6545030 4901 SRX7556560 SRS5993947 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.79469 0.0 0.15397 1.0 0.9847   0.52729 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56132 56132 SRR10887578 SRX7556559 SRS5993946 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CATATT: hair cells wt 4B7 GSM4271758   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CATATT: hair cells wt 4B7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271758 GSM4271758: CATATT: hair cells wt 4B7; Danio rerio; RNA Seq GSM4271758   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271758 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CATATT_r1.fq.gz GEO_CATATT_r2.fq.gz fastq fastq 2295744.0 34784.0 GSM4271758 r1 0:16 1:50 A:639356;C:454332;G:505930;T:695524;N:602 16 50     639356 454332 505930 695524 602 SRX7556559 SRS5993946 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.75545 0.0 0.11978 1.0 0.99239   0.47601 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56133 56133 SRR10887577 SRX7556558 SRS5993945 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ATAGTA: hair cells wt 4A12 GSM4271757   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ATAGTA: hair cells wt 4A12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271757 GSM4271757: ATAGTA: hair cells wt 4A12; Danio rerio; RNA Seq GSM4271757   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271757 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ATAGTA_r1.fq.gz GEO_ATAGTA_r2.fq.gz fastq fastq 29857542.0 452387.0 GSM4271757 r1 0:16 1:50 A:8650587;C:5671216;G:6756185;T:8771447;N:8107 16 50     8650587 5671216 6756185 8771447 8107 SRX7556558 SRS5993945 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.8678 0.0 0.0651 1.0 0.98502   0.43445 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56134 56134 SRR10887576 SRX7556557 SRS5993943 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ATAATG: hair cells wt 4A11 GSM4271756   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ATAATG: hair cells wt 4A11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271756 GSM4271756: ATAATG: hair cells wt 4A11; Danio rerio; RNA Seq GSM4271756   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271756 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ATAATG_r2.fq.gz GEO_ATAATG_r1.fq.gz fastq fastq 4178658.0 63313.0 GSM4271756 r1 0:16 1:50 A:1254421;C:788868;G:971659;T:1162609;N:1101 16 50     1254421 788868 971659 1162609 1101 SRX7556557 SRS5993943 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.70686 0.0 0.57365 1.0 0.99066   0.50095 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56135 56135 SRR10887575 SRX7556556 SRS5993942 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGTTAA: hair cells wt 4A10 GSM4271755   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGTTAA: hair cells wt 4A10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271755 GSM4271755: AGTTAA: hair cells wt 4A10; Danio rerio; RNA Seq GSM4271755   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271755 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGTTAA_r1.fq.gz GEO_AGTTAA_r2.fq.gz fastq fastq 34809588.0 527418.0 GSM4271755 r1 0:16 1:50 A:10137071;C:6623358;G:8098271;T:9941324;N:9564 16 50     10137071 6623358 8098271 9941324 9564 SRX7556556 SRS5993942 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.8522 0.0 0.06792 1.0 0.98577   0.39584 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56136 56136 SRR10887574 SRX7556555 SRS5993948 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGATAT: hair cells wt 4A9 GSM4271754   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGATAT: hair cells wt 4A9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271754 GSM4271754: AGATAT: hair cells wt 4A9; Danio rerio; RNA Seq GSM4271754   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271754 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGATAT_r2.fq.gz GEO_AGATAT_r1.fq.gz fastq fastq 28077060.0 425410.0 GSM4271754 r1 0:16 1:50 A:8318473;C:5276710;G:6472058;T:8001915;N:7904 16 50     8318473 5276710 6472058 8001915 7904 SRX7556555 SRS5993948 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86296 0.0 0.09442 1.0 0.98157   0.41782 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56137 56137 SRR10887573 SRX7556554 SRS5993941 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACTATT: hair cells wt 4A8 GSM4271753   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACTATT: hair cells wt 4A8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271753 GSM4271753: ACTATT: hair cells wt 4A8; Danio rerio; RNA Seq GSM4271753   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271753 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACTATT_r1.fq.gz GEO_ACTATT_r2.fq.gz fastq fastq 36810312.0 557732.0 GSM4271753 r1 0:16 1:50 A:10070588;C:7531734;G:7811902;T:11387603;N:8485 16 50     10070588 7531734 7811902 11387603 8485 SRX7556554 SRS5993941 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.87534 0.0 0.07813 1.0 0.98384   0.46263 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56138 56138 SRR10887572 SRX7556553 SRS5993944 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACAAAT: hair cells wt 4A7 GSM4271752   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACAAAT: hair cells wt 4A7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271752 GSM4271752: ACAAAT: hair cells wt 4A7; Danio rerio; RNA Seq GSM4271752   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271752 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACAAAT_r1.fq.gz GEO_ACAAAT_r2.fq.gz fastq fastq 75215184.0 1139624.0 GSM4271752 r1 0:16 1:50 A:22762180;C:15723998;G:17654105;T:19052173;N:22728 16 50     22762180 15723998 17654105 19052173 22728 SRX7556553 SRS5993944 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.69908 0.0 0.11765 1.0 0.97737   0.44964 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56139 56139 SRR10887571 SRX7556552 SRS5993939 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TGCCCC: hair cells wt 2H11 GSM4271751   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TGCCCC: hair cells wt 2H11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271751 GSM4271751: TGCCCC: hair cells wt 2H11; Danio rerio; RNA Seq GSM4271751   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271751 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TGCCCC_r1.fq.gz GEO_TGCCCC_r2.fq.gz fastq fastq 99705870.0 1510695.0 GSM4271751 r1 0:16 1:50 A:24784931;C:24938972;G:23296385;T:26663615;N:21967 16 50     24784931 24938972 23296385 26663615 21967 SRX7556552 SRS5993939 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.80511 0.0 0.11382 1.0 0.96601   0.44049 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56140 56140 SRR10887570 SRX7556551 SRS5993938 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCCGGG: hair cells wt 2H10 GSM4271750   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCCGGG: hair cells wt 2H10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271750 GSM4271750: TCCGGG: hair cells wt 2H10; Danio rerio; RNA Seq GSM4271750   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271750 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCCGGG_r1.fq.gz GEO_TCCGGG_r2.fq.gz fastq fastq 156814680.0 2375980.0 GSM4271750 r1 0:16 1:50 A:36405105;C:36084740;G:45725833;T:38559969;N:39033 16 50     36405105 36084740 45725833 38559969 39033 SRX7556551 SRS5993938 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.64184 0.0 0.13248 1.0 0.97745   0.55947 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56141 56141 SRR10887569 SRX7556550 SRS5993935 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GTGGCC: hair cells wt 2H9 GSM4271749   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GTGGCC: hair cells wt 2H9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271749 GSM4271749: GTGGCC: hair cells wt 2H9; Danio rerio; RNA Seq GSM4271749   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271749 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GTGGCC_r1.fq.gz GEO_GTGGCC_r2.fq.gz fastq fastq 10173966.0 154151.0 GSM4271749 r1 0:16 1:50 A:2501984;C:2250525;G:2956615;T:2462095;N:2747 16 50     2501984 2250525 2956615 2462095 2747 SRX7556550 SRS5993935 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.25254 0.0 0.11303 1.0 0.97701   0.51611 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56142 56142 SRR10887568 SRX7556549 SRS5993940 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GTCCCC: hair cells wt 2H8 GSM4271748   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GTCCCC: hair cells wt 2H8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271748 GSM4271748: GTCCCC: hair cells wt 2H8; Danio rerio; RNA Seq GSM4271748   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271748 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GTCCCC_r1.fq.gz GEO_GTCCCC_r2.fq.gz fastq fastq 88909656.0 1347116.0 GSM4271748 r1 0:16 1:50 A:22744809;C:21441987;G:19271731;T:25429628;N:21501 16 50     22744809 21441987 19271731 25429628 21501 SRX7556549 SRS5993940 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.89945 0.0 0.54925 1.0 0.97522   0.51973 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56143 56143 SRR10887567 SRX7556548 SRS5993936 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGGTGC: hair cells wt 2H7 GSM4271747   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGGTGC: hair cells wt 2H7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271747 GSM4271747: GGGTGC: hair cells wt 2H7; Danio rerio; RNA Seq GSM4271747   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271747 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGGTGC_r1.fq.gz GEO_GGGTGC_r2.fq.gz fastq fastq 49002294.0 742459.0 GSM4271747 r1 0:16 1:50 A:11795313;C:10365939;G:14029826;T:12796902;N:14314 16 50     11795313 10365939 14029826 12796902 14314 SRX7556548 SRS5993936 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.7657 0.0 0.10651 1.0 0.98167   0.52497 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56144 56144 SRR10887566 SRX7556547 SRS5993937 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCGGAG: hair cells wt 2G11 GSM4271746   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCGGAG: hair cells wt 2G11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271746 GSM4271746: GCGGAG: hair cells wt 2G11; Danio rerio; RNA Seq GSM4271746   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271746 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCGGAG_r1.fq.gz GEO_GCGGAG_r2.fq.gz fastq fastq 61406334.0 930399.0 GSM4271746 r1 0:16 1:50 A:16036263;C:12621880;G:17084575;T:15647426;N:16190 16 50     16036263 12621880 17084575 15647426 16190 SRX7556547 SRS5993937 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.82866 0.0 0.08484 1.0 0.97928   0.44046 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56145 56145 SRR10887565 SRX7556546 SRS5993934 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCGCAC: hair cells wt 2G10 GSM4271745   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCGCAC: hair cells wt 2G10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271745 GSM4271745: GCGCAC: hair cells wt 2G10; Danio rerio; RNA Seq GSM4271745   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271745 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCGCAC_r1.fq.gz GEO_GCGCAC_r2.fq.gz fastq fastq 103715700.0 1571450.0 GSM4271745 r1 0:16 1:50 A:27215760;C:23945117;G:26070541;T:26455572;N:28710 16 50     27215760 23945117 26070541 26455572 28710 SRX7556546 SRS5993934 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.85772 0.0 0.1198 1.0 0.9791   0.48025 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56146 56146 SRR10887564 SRX7556545 SRS5993930 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCCTCG: hair cells wt 2G9 GSM4271744   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCCTCG: hair cells wt 2G9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271744 GSM4271744: GCCTCG: hair cells wt 2G9; Danio rerio; RNA Seq GSM4271744   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271744 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCCTCG_r1.fq.gz GEO_GCCTCG_r2.fq.gz fastq fastq 23640144.0 358184.0 GSM4271744 r1 0:16 1:50 A:5894883;C:5651176;G:5830213;T:6257556;N:6316 16 50     5894883 5651176 5830213 6257556 6316 SRX7556545 SRS5993930 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.77455 0.0 0.09583 1.0 0.98315   0.43472 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56147 56147 SRR10887563 SRX7556544 SRS5993929 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCCGAC: hair cells wt 2G8 GSM4271743   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCCGAC: hair cells wt 2G8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271743 GSM4271743: GCCGAC: hair cells wt 2G8; Danio rerio; RNA Seq GSM4271743   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271743 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCCGAC_r1.fq.gz GEO_GCCGAC_r2.fq.gz fastq fastq 38128794.0 577709.0 GSM4271743 r1 0:16 1:50 A:9934273;C:9007484;G:9673915;T:9495594;N:17528 16 50     9934273 9007484 9673915 9495594 17528 SRX7556544 SRS5993929 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.77242 0.0 0.0868 1.0 0.98506   0.44418 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56148 56148 SRR10887562 SRX7556543 SRS5993932 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GCCCAG: hair cells wt 2G7 GSM4271742   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GCCCAG: hair cells wt 2G7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271742 GSM4271742: GCCCAG: hair cells wt 2G7; Danio rerio; RNA Seq GSM4271742   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271742 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GCCCAG_r1.fq.gz GEO_GCCCAG_r2.fq.gz fastq fastq 46788522.0 708917.0 GSM4271742 r1 0:16 1:50 A:12323933;C:10883758;G:11730463;T:11837342;N:13026 16 50     12323933 10883758 11730463 11837342 13026 SRX7556543 SRS5993932 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.77399 0.0 0.08918 1.0 0.98005   0.44547 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56149 56149 SRR10887561 SRX7556542 SRS5993927 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGGGGA: hair cells wt 2F12 GSM4271741   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGGGGA: hair cells wt 2F12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271741 GSM4271741: CGGGGA: hair cells wt 2F12; Danio rerio; RNA Seq GSM4271741   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271741 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGGGGA_r1.fq.gz GEO_CGGGGA_r2.fq.gz fastq fastq 29135040.0 441440.0 GSM4271741 r1 0:16 1:50 A:7693442;C:5930976;G:8161519;T:7339852;N:9251 16 50     7693442 5930976 8161519 7339852 9251 SRX7556542 SRS5993927 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.82074 0.0 0.11249 1.0 0.9763   0.41743 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56150 56150 SRR10887560 SRX7556541 SRS5993926 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGGCGT: hair cells wt 2F11 GSM4271740   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGGCGT: hair cells wt 2F11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271740 GSM4271740: CGGCGT: hair cells wt 2F11; Danio rerio; RNA Seq GSM4271740   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271740 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGGCGT_r1.fq.gz GEO_CGGCGT_r2.fq.gz fastq fastq 53204382.0 806127.0 GSM4271740 r1 0:16 1:50 A:13239467;C:11643256;G:14105165;T:14200599;N:15895 16 50     13239467 11643256 14105165 14200599 15895 SRX7556541 SRS5993926 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.78045 0.0 0.08602 1.0 0.98171   0.42093 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56151 56151 SRR10887559 SRX7556540 SRS5993933 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGGACG: hair cells wt 2F10 GSM4271739   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGGACG: hair cells wt 2F10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271739 GSM4271739: CGGACG: hair cells wt 2F10; Danio rerio; RNA Seq GSM4271739   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271739 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGGACG_r1.fq.gz GEO_CGGACG_r2.fq.gz fastq fastq 113671008.0 1722288.0 GSM4271739 r1 0:16 1:50 A:30256021;C:24026594;G:29758029;T:29596584;N:33780 16 50     30256021 24026594 29758029 29596584 33780 SRX7556540 SRS5993933 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.87614 0.0 0.14295 1.0 0.97688   0.48159 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56152 56152 SRR10887558 SRX7556539 SRS5993928 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGCGGT: hair cells wt 2F9 GSM4271738   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGCGGT: hair cells wt 2F9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271738 GSM4271738: CGCGGT: hair cells wt 2F9; Danio rerio; RNA Seq GSM4271738   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271738 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGCGGT_r1.fq.gz GEO_CGCGGT_r2.fq.gz fastq fastq 59444088.0 900668.0 GSM4271738 r1 0:16 1:50 A:14758639;C:12847168;G:15472154;T:16349050;N:17077 16 50     14758639 12847168 15472154 16349050 17077 SRX7556539 SRS5993928 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.85772 0.0 0.06994 1.0 0.98027   0.44563 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56153 56153 SRR10887557 SRX7556538 SRS5993925 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGCCGA: hair cells wt 2F8 GSM4271737   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGCCGA: hair cells wt 2F8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271737 GSM4271737: CGCCGA: hair cells wt 2F8; Danio rerio; RNA Seq GSM4271737   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271737 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGCCGA_r1.fq.gz GEO_CGCCGA_r2.fq.gz fastq fastq 58332450.0 883825.0 GSM4271737 r1 0:16 1:50 A:15100292;C:13840300;G:15452320;T:13923439;N:16099 16 50     15100292 13840300 15452320 13923439 16099 SRX7556538 SRS5993925 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.72198 0.0 0.09689 1.0 0.98119   0.42056 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56154 56154 SRR10887556 SRX7556537 SRS5993923 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CGCACC: hair cells wt 2F7 GSM4271736   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CGCACC: hair cells wt 2F7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271736 GSM4271736: CGCACC: hair cells wt 2F7; Danio rerio; RNA Seq GSM4271736   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271736 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CGCACC_r1.fq.gz GEO_CGCACC_r2.fq.gz fastq fastq 59064720.0 894920.0 GSM4271736 r1 0:16 1:50 A:15436523;C:14686266;G:14017782;T:14906469;N:17680 16 50     15436523 14686266 14017782 14906469 17680 SRX7556537 SRS5993923 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81502 0.0 0.16399 1.0 0.97847   0.41105 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56155 56155 SRR10887555 SRX7556536 SRS5993921 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CCACCG: hair cells wt 2E12 GSM4271735   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CCACCG: hair cells wt 2E12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271735 GSM4271735: CCACCG: hair cells wt 2E12; Danio rerio; RNA Seq GSM4271735   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271735 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CCACCG_r1.fq.gz GEO_CCACCG_r2.fq.gz fastq fastq 28334064.0 429304.0 GSM4271735 r1 0:16 1:50 A:7520223;C:7025285;G:6745861;T:7033764;N:8931 16 50     7520223 7025285 6745861 7033764 8931 SRX7556536 SRS5993921 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.80711 0.0 0.10281 1.0 0.97968   0.36993 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56156 56156 SRR10887554 SRX7556535 SRS5993920 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CAGCCG: hair cells wt 2E11 GSM4271734   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CAGCCG: hair cells wt 2E11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271734 GSM4271734: CAGCCG: hair cells wt 2E11; Danio rerio; RNA Seq GSM4271734   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271734 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CAGCCG_r1.fq.gz GEO_CAGCCG_r2.fq.gz fastq fastq 76943724.0 1165814.0 GSM4271734 r1 0:16 1:50 A:20252257;C:18252609;G:19289676;T:19127181;N:22001 16 50     20252257 18252609 19289676 19127181 22001 SRX7556535 SRS5993920 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.82968 0.0 0.07998 1.0 0.98098   0.47591 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56157 56157 SRR10887553 SRX7556534 SRS5993919 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CACCCC: hair cells wt 2E10 GSM4271733   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CACCCC: hair cells wt 2E10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271733 GSM4271733: CACCCC: hair cells wt 2E10; Danio rerio; RNA Seq GSM4271733   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271733 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CACCCC_r1.fq.gz GEO_CACCCC_r2.fq.gz fastq fastq 59700300.0 904550.0 GSM4271733 r1 0:16 1:50 A:15645395;C:15522037;G:13562532;T:14955831;N:14505 16 50     15645395 15522037 13562532 14955831 14505 SRX7556534 SRS5993919 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.74633 0.0 0.15499 1.0 0.97084   0.51247 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56158 56158 SRR10887552 SRX7556533 SRS5993924 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGGCCC: hair cells wt 2E9 GSM4271732   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGGCCC: hair cells wt 2E9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271732 GSM4271732: AGGCCC: hair cells wt 2E9; Danio rerio; RNA Seq GSM4271732   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271732 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGGCCC_r1.fq.gz GEO_AGGCCC_r2.fq.gz fastq fastq 247661106.0 3752441.0 GSM4271732 r1 0:16 1:50 A:60796649;C:61932057;G:69774659;T:55097229;N:60512 16 50     60796649 61932057 69774659 55097229 60512 SRX7556533 SRS5993924 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.67963 0.0 0.14932 1.0 0.9656   0.55686 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56159 56159 SRR10887551 SRX7556532 SRS5993918 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGCCCG: hair cells wt 2E8 GSM4271731   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGCCCG: hair cells wt 2E8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271731 GSM4271731: AGCCCG: hair cells wt 2E8; Danio rerio; RNA Seq GSM4271731   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271731 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGCCCG_r1.fq.gz GEO_AGCCCG_r2.fq.gz fastq fastq 85194054.0 1290819.0 GSM4271731 r1 0:16 1:50 A:21886276;C:20333936;G:22929730;T:20024600;N:19512 16 50     21886276 20333936 22929730 20024600 19512 SRX7556532 SRS5993918 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.77493 0.0 0.12576 1.0 0.97007   0.54242 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56160 56160 SRR10887550 SRX7556531 SRS5993931 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACGCCG: hair cells wt 2E7 GSM4271730   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACGCCG: hair cells wt 2E7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271730 GSM4271730: ACGCCG: hair cells wt 2E7; Danio rerio; RNA Seq GSM4271730   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271730 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACGCCG_r1.fq.gz GEO_ACGCCG_r2.fq.gz fastq fastq 16576230.0 251155.0 GSM4271730 r1 0:16 1:50 A:4101131;C:3992983;G:4977837;T:3500149;N:4130 16 50     4101131 3992983 4977837 3500149 4130 SRX7556531 SRS5993931 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.22521 0.0 0.11583 1.0 0.97652   0.49987 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56161 56161 SRR10887549 SRX7556530 SRS5993922 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CTTCTG: hair cells wt 2D12 GSM4271729   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CTTCTG: hair cells wt 2D12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271729 GSM4271729: CTTCTG: hair cells wt 2D12; Danio rerio; RNA Seq GSM4271729   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271729 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CTTCTG_r1.fq.gz GEO_CTTCTG_r2.fq.gz fastq fastq 10296198.0 156003.0 GSM4271729 r1 0:16 1:50 A:2532051;C:2299039;G:2378957;T:3082993;N:3158 16 50     2532051 2299039 2378957 3082993 3158 SRX7556530 SRS5993922 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.8312 0.0 0.10552 1.0 0.98271   0.50933 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56162 56162 SRR10887548 SRX7556529 SRS5993916 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CCGATT: hair cells wt 2D11 GSM4271728   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CCGATT: hair cells wt 2D11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271728 GSM4271728: CCGATT: hair cells wt 2D11; Danio rerio; RNA Seq GSM4271728   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271728 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CCGATT_r1.fq.gz GEO_CCGATT_r2.fq.gz fastq fastq 62508666.0 947101.0 GSM4271728 r1 0:16 1:50 A:16582399;C:13664923;G:14482786;T:17761639;N:16919 16 50     16582399 13664923 14482786 17761639 16919 SRX7556529 SRS5993916 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88829 0.0 0.24871 1.0 0.98171   0.52749 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56163 56163 SRR10887547 SRX7556528 SRS5993915 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CAGTCA: hair cells wt 2D10 GSM4271727   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CAGTCA: hair cells wt 2D10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271727 GSM4271727: CAGTCA: hair cells wt 2D10; Danio rerio; RNA Seq GSM4271727   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271727 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CAGTCA_r1.fq.gz GEO_CAGTCA_r2.fq.gz fastq fastq 81890886.0 1240771.0 GSM4271727 r1 0:16 1:50 A:22385298;C:18267104;G:18858387;T:22355623;N:24474 16 50     22385298 18267104 18858387 22355623 24474 SRX7556528 SRS5993915 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.84616 0.0 0.08088 1.0 0.98121   0.43702 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56164 56164 SRR10887546 SRX7556527 SRS5993912 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGGGAT: hair cells wt 2D9 GSM4271726   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGGGAT: hair cells wt 2D9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271726 GSM4271726: AGGGAT: hair cells wt 2D9; Danio rerio; RNA Seq GSM4271726   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271726 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGGGAT_r1.fq.gz GEO_AGGGAT_r2.fq.gz fastq fastq 27941364.0 423354.0 GSM4271726 r1 0:16 1:50 A:7658771;C:5529411;G:7466727;T:7278034;N:8421 16 50     7658771 5529411 7466727 7278034 8421 SRX7556527 SRS5993912 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.71935 0.0 0.14115 1.0 0.98021   0.39706 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56165 56165 SRR10887545 SRX7556526 SRS5993917 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCTTTC: hair cells wt 2D8 GSM4271725   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCTTTC: hair cells wt 2D8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271725 GSM4271725: TCTTTC: hair cells wt 2D8; Danio rerio; RNA Seq GSM4271725   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271725 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCTTTC_r1.fq.gz GEO_TCTTTC_r2.fq.gz fastq fastq 39611286.0 600171.0 GSM4271725 r1 0:16 1:50 A:9593653;C:8891817;G:9379515;T:11735763;N:10538 16 50     9593653 8891817 9379515 11735763 10538 SRX7556526 SRS5993917 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.7029 0.0 0.09623 1.0 0.98005   0.5794 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56166 56166 SRR10887544 SRX7556525 SRS5993911 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TTTGTA: hair cells wt 2D7 GSM4271724   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TTTGTA: hair cells wt 2D7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271724 GSM4271724: TTTGTA: hair cells wt 2D7; Danio rerio; RNA Seq GSM4271724   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271724 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TTTGTA_r1.fq.gz GEO_TTTGTA_r2.fq.gz fastq fastq 45225048.0 685228.0 GSM4271724 r1 0:16 1:50 A:11889541;C:8360740;G:10779684;T:14183435;N:11648 16 50     11889541 8360740 10779684 14183435 11648 SRX7556525 SRS5993911 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81562 0.0 0.09419 1.0 0.97916   0.51242 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56167 56167 SRR10887543 SRX7556524 SRS5993910 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TGTAAA: hair cells wt 2C12 GSM4271723   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TGTAAA: hair cells wt 2C12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271723 GSM4271723: TGTAAA: hair cells wt 2C12; Danio rerio; RNA Seq GSM4271723   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271723 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TGTAAA_r1.fq.gz GEO_TGTAAA_r2.fq.gz fastq fastq 36393456.0 551416.0 GSM4271723 r1 0:16 1:50 A:10494740;C:6916737;G:8340339;T:10629953;N:11687 16 50     10494740 6916737 8340339 10629953 11687 SRX7556524 SRS5993910 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88673 0.0 0.07491 1.0 0.9867   0.42572 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56168 56168 SRR10887542 SRX7556523 SRS5993909 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TGAAAT: hair cells wt 2C11 GSM4271722   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TGAAAT: hair cells wt 2C11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271722 GSM4271722: TGAAAT: hair cells wt 2C11; Danio rerio; RNA Seq GSM4271722   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271722 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TGAAAT_r1.fq.gz GEO_TGAAAT_r2.fq.gz fastq fastq 59922720.0 907920.0 GSM4271722 r1 0:16 1:50 A:17660178;C:11271616;G:13597589;T:17378574;N:14763 16 50     17660178 11271616 13597589 17378574 14763 SRX7556523 SRS5993909 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86668 0.0 0.13202 1.0 0.98466   0.47258 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56169 56169 SRR10887541 SRX7556522 SRS5993914 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TCATTA: hair cells wt 2C10 GSM4271721   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TCATTA: hair cells wt 2C10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271721 GSM4271721: TCATTA: hair cells wt 2C10; Danio rerio; RNA Seq GSM4271721   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271721 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TCATTA_r1.fq.gz GEO_TCATTA_r2.fq.gz fastq fastq 46021734.0 697299.0 GSM4271721 r1 0:16 1:50 A:12725573;C:9548168;G:10202938;T:13533019;N:12036 16 50     12725573 9548168 10202938 13533019 12036 SRX7556522 SRS5993914 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.79991 0.0 0.12416 1.0 0.98285   0.51119 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56170 56170 SRR10887540 SRX7556521 SRS5993907 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TATTTG: hair cells wt 2C9 GSM4271720   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TATTTG: hair cells wt 2C9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271720 GSM4271720: TATTTG: hair cells wt 2C9; Danio rerio; RNA Seq GSM4271720   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271720 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TATTTG_r1.fq.gz GEO_TATTTG_r2.fq.gz fastq fastq 57077328.0 864808.0 GSM4271720 r1 0:16 1:50 A:15095956;C:10660095;G:12874801;T:18430756;N:15720 16 50     15095956 10660095 12874801 18430756 15720 SRX7556521 SRS5993907 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.83235 0.0 0.08647 1.0 0.98411   0.4321 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56171 56171 SRR10887539 SRX7556520 SRS5993906 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TATGTT: hair cells wt 2C8 GSM4271719   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TATGTT: hair cells wt 2C8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271719 GSM4271719: TATGTT: hair cells wt 2C8; Danio rerio; RNA Seq GSM4271719   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271719 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TATGTT_r1.fq.gz GEO_TATGTT_r2.fq.gz fastq fastq 82334538.0 1247493.0 GSM4271719 r1 0:16 1:50 A:21259201;C:15330189;G:20495066;T:25226866;N:23216 16 50     21259201 15330189 20495066 25226866 23216 SRX7556520 SRS5993906 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.82387 0.0 0.08807 1.0 0.97707   0.53859 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56172 56172 SRR10887538 SRX7556519 SRS5993904 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   TATATC: hair cells wt 2C7 GSM4271718   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf TATATC: hair cells wt 2C7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271718 GSM4271718: TATATC: hair cells wt 2C7; Danio rerio; RNA Seq GSM4271718   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271718 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_TATATC_r1.fq.gz GEO_TATATC_r2.fq.gz fastq fastq 47552802.0 720497.0 GSM4271718 r1 0:16 1:50 A:13161599;C:9865238;G:10361619;T:14152235;N:12111 16 50     13161599 9865238 10361619 14152235 12111 SRX7556519 SRS5993904 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.80675 0.0 0.09336 1.0 0.98466   0.43652 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Multi-stage Multi-stage Lateral Line Sensory System
56173 56173 SRR10887537 SRX7556518 SRS5993903 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GTATAA: hair cells wt 2B12 GSM4271717   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GTATAA: hair cells wt 2B12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271717 GSM4271717: GTATAA: hair cells wt 2B12; Danio rerio; RNA Seq GSM4271717   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271717 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GTATAA_r1.fq.gz GEO_GTATAA_r2.fq.gz fastq fastq 105576240.0 1599640.0 GSM4271717 r1 0:16 1:50 A:30487024;C:19765998;G:24257759;T:31040963;N:24496 16 50     30487024 19765998 24257759 31040963 24496 SRX7556518 SRS5993903 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.8655 0.0 0.10874 1.0 0.97729   0.45045 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56174 56174 SRR10887536 SRX7556517 SRS5993902 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GATATA: hair cells wt 2B11 GSM4271716   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GATATA: hair cells wt 2B11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271716 GSM4271716: GATATA: hair cells wt 2B11; Danio rerio; RNA Seq GSM4271716   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271716 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GATATA_r1.fq.gz GEO_GATATA_r2.fq.gz fastq fastq 131727882.0 1995877.0 GSM4271716 r1 0:16 1:50 A:39145090;C:25049441;G:28985366;T:38514286;N:33699 16 50     39145090 25049441 28985366 38514286 33699 SRX7556517 SRS5993902 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.91406 0.0 0.57766 1.0 0.98425   0.43543 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56175 56175 SRR10887535 SRX7556516 SRS5993901 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GAAATT: hair cells wt 2B10 GSM4271715   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GAAATT: hair cells wt 2B10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271715 GSM4271715: GAAATT: hair cells wt 2B10; Danio rerio; RNA Seq GSM4271715   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271715 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GAAATT_r1.fq.gz GEO_GAAATT_r2.fq.gz fastq fastq 33507144.0 507684.0 GSM4271715 r1 0:16 1:50 A:9768700;C:6465594;G:7741672;T:9522644;N:8534 16 50     9768700 6465594 7741672 9522644 8534 SRX7556516 SRS5993901 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.7961 0.0 0.12613 1.0 0.98169   0.50881 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56176 56176 SRR10887534 SRX7556515 SRS5993908 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CTATTA: hair cells wt 2B9 GSM4271714   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CTATTA: hair cells wt 2B9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271714 GSM4271714: CTATTA: hair cells wt 2B9; Danio rerio; RNA Seq GSM4271714   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271714 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CTATTA_r1.fq.gz GEO_CTATTA_r2.fq.gz fastq fastq 48644112.0 737032.0 GSM4271714 r1 0:16 1:50 A:13431743;C:10100159;G:10510510;T:14590743;N:10957 16 50     13431743 10100159 10510510 14590743 10957 SRX7556515 SRS5993908 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.82941 0.0 0.09209 1.0 0.98171   0.48275 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56177 56177 SRR10887533 SRX7556514 SRS5993913 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CATTTA: hair cells wt 2B8 GSM4271713   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CATTTA: hair cells wt 2B8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271713 GSM4271713: CATTTA: hair cells wt 2B8; Danio rerio; RNA Seq GSM4271713   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271713 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CATTTA_r1.fq.gz GEO_CATTTA_r2.fq.gz fastq fastq 149976486.0 2272371.0 GSM4271713 r1 0:16 1:50 A:42208515;C:30318978;G:31462869;T:45953123;N:33001 16 50     42208515 30318978 31462869 45953123 33001 SRX7556514 SRS5993913 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.87297 0.0 0.07359 1.0 0.97839   0.41133 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56178 56178 SRR10887532 SRX7556513 SRS5993900 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   CAATAA: hair cells wt 2B7 GSM4271712   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf CAATAA: hair cells wt 2B7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271712 GSM4271712: CAATAA: hair cells wt 2B7; Danio rerio; RNA Seq GSM4271712   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271712 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_CAATAA_r1.fq.gz GEO_CAATAA_r2.fq.gz fastq fastq 57412542.0 869887.0 GSM4271712 r1 0:16 1:50 A:17908670;C:11429509;G:11963221;T:16094209;N:16933 16 50     17908670 11429509 11963221 16094209 16933 SRX7556513 SRS5993900 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.84753 0.0 0.12124 1.0 0.98427   0.40643 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56179 56179 SRR10887531 SRX7556512 SRS5993905 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ATACTT: hair cells wt 2A12 GSM4271711   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ATACTT: hair cells wt 2A12 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271711 GSM4271711: ATACTT: hair cells wt 2A12; Danio rerio; RNA Seq GSM4271711   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271711 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ATACTT_r1.fq.gz GEO_ATACTT_r2.fq.gz fastq fastq 8651148.0 131078.0 GSM4271711 r1 0:16 1:50 A:2330634;C:1784107;G:2159176;T:2374901;N:2330 16 50     2330634 1784107 2159176 2374901 2330 SRX7556512 SRS5993905 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.29454 0.0 0.1535 1.0 0.9865   0.65013 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56180 56180 SRR10887530 SRX7556511 SRS5993898 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ATAACA: hair cells wt 2A11 GSM4271710   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ATAACA: hair cells wt 2A11 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271710 GSM4271710: ATAACA: hair cells wt 2A11; Danio rerio; RNA Seq GSM4271710   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271710 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ATAACA_r1.fq.gz GEO_ATAACA_r2.fq.gz fastq fastq 58610706.0 888041.0 GSM4271710 r1 0:16 1:50 A:18014874;C:11661118;G:12339527;T:16578759;N:16428 16 50     18014874 11661118 12339527 16578759 16428 SRX7556511 SRS5993898 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81794 0.0 0.0639 1.0 0.98563   0.46396 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56181 56181 SRR10887529 SRX7556510 SRS5993897 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AGTAAT: hair cells wt 2A10 GSM4271709   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AGTAAT: hair cells wt 2A10 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271709 GSM4271709: AGTAAT: hair cells wt 2A10; Danio rerio; RNA Seq GSM4271709   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271709 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AGTAAT_r1.fq.gz GEO_AGTAAT_r2.fq.gz fastq fastq 111276594.0 1686009.0 GSM4271709 r1 0:16 1:50 A:32926054;C:20521030;G:24191119;T:33604147;N:34244 16 50     32926054 20521030 24191119 33604147 34244 SRX7556510 SRS5993897 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.88188 0.0 0.14223 1.0 0.98005   0.44365 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56182 56182 SRR10887528 SRX7556509 SRS5993896 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACTTTA: hair cells wt 2A9 GSM4271708   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACTTTA: hair cells wt 2A9 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271708 GSM4271708: ACTTTA: hair cells wt 2A9; Danio rerio; RNA Seq GSM4271708   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271708 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACTTTA_r1.fq.gz GEO_ACTTTA_r2.fq.gz fastq fastq 61468308.0 931338.0 GSM4271708 r1 0:16 1:50 A:17145659;C:12322061;G:13013829;T:18971733;N:15026 16 50     17145659 12322061 13013829 18971733 15026 SRX7556509 SRS5993896 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.79407 0.0 0.09895 1.0 0.98313   0.41971 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56183 56183 SRR10887527 SRX7556508 SRS5993894 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   ACATAA: hair cells wt 2A8 GSM4271707   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf ACATAA: hair cells wt 2A8 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271707 GSM4271707: ACATAA: hair cells wt 2A8; Danio rerio; RNA Seq GSM4271707   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271707 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_ACATAA_r1.fq.gz GEO_ACATAA_r2.fq.gz fastq fastq 158605656.0 2403116.0 GSM4271707 r1 0:16 1:50 A:49247323;C:32258174;G:34033114;T:43023807;N:43238 16 50     49247323 32258174 34033114 43023807 43238 SRX7556508 SRS5993894 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81999 0.0 0.11125 1.0 0.97904   0.47654 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56184 56184 SRR10887526 SRX7556507 SRS5993899 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   AATTGA: hair cells wt 2A7 GSM4271706   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf AATTGA: hair cells wt 2A7 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] wild type|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271706 GSM4271706: AATTGA: hair cells wt 2A7; Danio rerio; RNA Seq GSM4271706   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271706 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_AATTGA_r1.fq.gz GEO_AATTGA_r2.fq.gz fastq fastq 51021498.0 773053.0 GSM4271706 r1 0:16 1:50 A:14658299;C:10020932;G:12806777;T:13520360;N:15130 16 50     14658299 10020932 12806777 13520360 15130 SRX7556507 SRS5993899 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.5837 0.0 0.13118 1.0 0.98324   0.53616 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56185 56185 SRR10887525 SRX7556506 SRS5993892 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGGCTC: hair cells Emx2 mutant 4H5 GSM4271705   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGGCTC: hair cells Emx2 mutant 4H5 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271705 GSM4271705: GGGCTC: hair cells Emx2 mutant 4H5; Danio rerio; RNA Seq GSM4271705   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271705 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGGCTC_r1.fq.gz GEO_GGGCTC_r2.fq.gz fastq fastq 14613588.0 221418.0 GSM4271705 r1 0:16 1:50 A:3780247;C:3111579;G:3578982;T:4138632;N:4148 16 50     3780247 3111579 3578982 4138632 4148 SRX7556506 SRS5993892 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.79993 0.0 0.32776 1.0 0.98088   0.70912 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56186 56186 SRR10887524 SRX7556505 SRS5993891 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGGAGG: hair cells Emx2 mutant 4H4 GSM4271704   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGGAGG: hair cells Emx2 mutant 4H4 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271704 GSM4271704: GGGAGG: hair cells Emx2 mutant 4H4; Danio rerio; RNA Seq GSM4271704   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271704 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGGAGG_r1.fq.gz GEO_GGGAGG_r2.fq.gz fastq fastq 34179090.0 517865.0 GSM4271704 r1 0:16 1:50 A:8876876;C:6632469;G:9978089;T:8681433;N:10223 16 50     8876876 6632469 9978089 8681433 10223 SRX7556505 SRS5993891 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.81313 0.0 0.10872 1.0 0.98048   0.43457 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56187 56187 SRR10887523 SRX7556504 SRS5993889 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGCGGA: hair cells Emx2 mutant 4H3 GSM4271703   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGCGGA: hair cells Emx2 mutant 4H3 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271703 GSM4271703: GGCGGA: hair cells Emx2 mutant 4H3; Danio rerio; RNA Seq GSM4271703   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271703 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGCGGA_r1.fq.gz GEO_GGCGGA_r2.fq.gz fastq fastq 17174256.0 260216.0 GSM4271703 r1 0:16 1:50 A:4522091;C:3638319;G:4502523;T:4506468;N:4855 16 50     4522091 3638319 4502523 4506468 4855 SRX7556504 SRS5993889 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.86777 0.0 0.20114 1.0 0.98725   0.43401 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56188 56188 SRR10887522 SRX7556503 SRS5993893 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGCAGC: hair cells Emx2 mutant 4H2 GSM4271702   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGCAGC: hair cells Emx2 mutant 4H2 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271702 GSM4271702: GGCAGC: hair cells Emx2 mutant 4H2; Danio rerio; RNA Seq GSM4271702   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271702 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGCAGC_r1.fq.gz GEO_GGCAGC_r2.fq.gz fastq fastq 16047438.0 243143.0 GSM4271702 r1 0:16 1:50 A:4221078;C:3522951;G:4111148;T:4187493;N:4768 16 50     4221078 3522951 4111148 4187493 4768 SRX7556503 SRS5993893 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.85088 0.0 0.19676 1.0 0.98397   0.40778 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System
56189 56189 SRR10887521 SRX7556502 SRS5993888 SRP241937 PRJNA601204 Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 GSE143663 Transcriptome Analysis This dataset consists of single cell RNA seq mcSCRBseq data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral line neuromast hair cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of wild type and Emx2 mutant Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs. Overall design: mcSCRB seq experiment of hair cells from wild type and Emx2 mutant larvae.   pubmed:32109392   GGACGC: hair cells Emx2 mutant 4H1 GSM4271701   source name:zebrafish neuromast hair cells|genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GGACGC: hair cells Emx2 mutant 4H1 Fastq reads were processed with the zUMIs pipeline version 0.2.0 Parekh et al. 2018 cDNA reads were aligned to the Zebrafish Genome GRCZ11 with STAR 2.6.0a Quantification was done with ENSEMBL gene model GRCz11.94 Genome build: Zebrafish: GRCz11 Ensembl 94 Supplementary files format and content: cell columns and gene rows wise UMI expression table zebrafish neuromast hair cells none Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. genotype:Tg[myo6b:actb1 EGFP] Emx2 mutant|tissue:zebrafish neuromast hair cells|developmental day:6 dpf GSM4271701 GSM4271701: GGACGC: hair cells Emx2 mutant 4H1; Danio rerio; RNA Seq GSM4271701   1 Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. mcSCRB seq Bagnoli et al. 2018 GEO Accession:GSM4271701 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP241937     GEO_GGACGC_r1.fq.gz GEO_GGACGC_r2.fq.gz fastq fastq 30919614.0 468479.0 GSM4271701 r1 0:16 1:50 A:8053777;C:6811479;G:8162913;T:7881989;N:9456 16 50     8053777 6811479 8162913 7881989 9456 SRX7556502 SRS5993888 SRA1026350 GEO Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München 2 0.0 0.78988 0.0 0.07194 1.0 0.98537   0.41105 16 50 T B sc-like readlen illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2020-01-14 Larval Larval Lateral Line Sensory System

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