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12 rows where devstage_curation = "Multi-stage" and tissue_curation = "Lateral Line"

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tissue_curation_coarse 1

tissue_curation 1

  • Lateral Line · 12 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Multi-stage · 12 ✖
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
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
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

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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");;