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 66962,SRR16912780,SRX13105209,SRS11041502,SRP345473,PRJNA779441,Single Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum,PRJNA779441,Other,The optic tectum OT is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus the OT is responsible for the reception and integration of stimuli followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades less is known concerning specific cell types microcircuitry and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single cell RNA sequencing scRNA seq to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Etcfos:Gal4;UAS:Kaede. We sequenced 13 320 cells a 4X cellular coverage and identified 25 putative OT cell populations. Within those cells we identified several mature and developing neuronal populations as well as non neuronal cell types including oligodendrocytes microglia and radial glia. Although most mature neurons demonstrate GABAergic activity several glutamatergic populations are present as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes and computed RNA velocity to infer current and future transcriptional cell states. Finally we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge this is the first time scRNA seq has been applied to explore the OT alone and in depth.,,,,,Optic Tectum Run 2,,strain:y304Etcfos:Gal4; UAS:Kaede|age:7dpf|dev stage:Larval|sex:Unknown|tissue:Kaede+ midbrain cells|sample type:Methanol fixed FAC sorted cells|Run Number:2|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: larval optic tectum,18798R,18798R,10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP345473,,,18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_I1_001.fastq.gz 18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_I2_001.fastq.gz 18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_R1_001.fastq.gz 18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,51241551174.0,258795713.0,18798X1 210405 A00421 0312 BHYYKVDSXY S1 L004 I1 001.fastq.gz,0:10 1:10 2:28 3:150,A:11347233208;C:8190548246;G:9193124724;T:10088035538;N:415234,10,10,28,150,11347233208,8190548246,9193124724,10088035538,415234,SRX13105209,SRS11041502,SRA1327223,Brigham Young University|Cell Biology and Physiology,Brigham Young University,1,0.87747,,0.31462,,0.80095,,0.57402,,150,,B,,usable mapping rate,illumina,novaseq_era,3prime,other,unknown,sc,single_cell_droplet,10x,,United States,2021-11-10,Larval,Larval,Brain,Nervous System 66963,SRR16912781,SRX13105208,SRS11041501,SRP345473,PRJNA779441,Single Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum,PRJNA779441,Other,The optic tectum OT is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus the OT is responsible for the reception and integration of stimuli followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades less is known concerning specific cell types microcircuitry and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single cell RNA sequencing scRNA seq to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Etcfos:Gal4;UAS:Kaede. We sequenced 13 320 cells a 4X cellular coverage and identified 25 putative OT cell populations. Within those cells we identified several mature and developing neuronal populations as well as non neuronal cell types including oligodendrocytes microglia and radial glia. Although most mature neurons demonstrate GABAergic activity several glutamatergic populations are present as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes and computed RNA velocity to infer current and future transcriptional cell states. Finally we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge this is the first time scRNA seq has been applied to explore the OT alone and in depth.,,,,,Optic Tectum Run 1,,strain:y304Etcfos:Gal4; UAS:Kaede|age:7dpf|dev stage:Larval|sex:Unknown|tissue:Kaede+ midbrain cells|sample type:Methanol fixed FAC sorted cells|Run Number:1|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: larval optic tectum,18507R,18507R,10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP345473,,,18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_I1_001.fastq.gz 18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_I2_001.fastq.gz 18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_R1_001.fastq.gz 18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,64682907300.0,326681350.0,18507X1 201113 A00421 0256 BHLY3JDSXY S5 L003 I1 001.fastq.gz,0:10 1:10 2:28 3:150,A:14518921141;C:9982364575;G:11381145187;T:13119455374;N:316223,10,10,28,150,14518921141,9982364575,11381145187,13119455374,316223,SRX13105208,SRS11041501,SRA1327223,Brigham Young University|Cell Biology and Physiology,Brigham Young University,1,0.87166,,0.34827,,0.82298,,0.60301,,150,,B,,usable mapping rate,illumina,novaseq_era,3prime,other,unknown,sc,single_cell_droplet,10x,,United States,2021-11-11,Larval,Larval,Brain,Nervous System 75288,SRR25598371,SRX21326033,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R6,3124R6,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F1-5_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L002_R1_001.fastq.gz 3124F1-5_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L002_R2_001.fastq.gz,fastq fastq,10700303544.0,127384566.0,3124F1 5 220322 A01563 0038 AHY3YHDRXY GCAGTATAGG GTGCACGGAA L002 R1 001.fastq.gz,0:28 1:56,A:3095737110;C:2216347626;G:2244897948;T:3142928946;N:391914,28,56,,,3095737110,2216347626,2244897948,3142928946,391914,SRX21326033,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00785,0.88899,0.00393,0.43423,0.99017,0.7486,0.36074,0.50405,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System 75289,SRR25598372,SRX21326032,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R5,3124R5,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F2-5_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L002_R1_001.fastq.gz 3124F2-5_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L002_R2_001.fastq.gz,fastq fastq,15103664688.0,179805532.0,3124F2 5 220322 A01563 0038 AHY3YHDRXY AACCACGCAT TAACCTGAAT L002 R1 001.fastq.gz,0:28 1:56,A:4376559806;C:3122875667;G:3166215898;T:4437453369;N:559948,28,56,,,4376559806,3122875667,3166215898,4437453369,559948,SRX21326032,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00779,0.88709,0.00398,0.43543,0.98973,0.74736,0.35685,0.49938,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System 75290,SRR25598373,SRX21326031,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R4,3124R4,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F3-5_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L002_R1_001.fastq.gz 3124F3-5_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L002_R2_001.fastq.gz,fastq fastq,11678915220.0,139034705.0,3124F3 5 220322 A01563 0038 AHY3YHDRXY CCCACCACAA AAGCGGAGGT L002 R1 001.fastq.gz,0:28 1:56,A:3362125535;C:2431029106;G:2460479617;T:3424857950;N:423012,28,56,,,3362125535,2431029106,2460479617,3424857950,423012,SRX21326031,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00813,0.89215,0.00415,0.42908,0.99028,0.74651,0.33376,0.49996,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System 75291,SRR25598374,SRX21326030,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R3,3124R3,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F1-1_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L001_R1_001.fastq.gz 3124F1-1_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L001_R2_001.fastq.gz,fastq fastq,22921793076.0,272878489.0,3124F1 1 220322 A01563 0038 AHY3YHDRXY GCAGTATAGG GTGCACGGAA L001 R1 001.fastq.gz,0:28 1:56,A:6639916156;C:4743377942;G:4802115704;T:6735725053;N:658221,28,56,,,6639916156,4743377942,4802115704,6735725053,658221,SRX21326030,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00785,0.88789,0.00408,0.43253,0.99003,0.74722,0.39124,0.51078,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System 75292,SRR25598375,SRX21326029,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R2,3124R2,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F2-1_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L001_R1_001.fastq.gz 3124F2-1_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L001_R2_001.fastq.gz,fastq fastq,32435983776.0,386142664.0,3124F2 1 220322 A01563 0038 AHY3YHDRXY AACCACGCAT TAACCTGAAT L001 R1 001.fastq.gz,0:28 1:56,A:9417269653;C:6700846098;G:6786259472;T:9530672341;N:936212,28,56,,,9417269653,6700846098,6786259472,9530672341,936212,SRX21326029,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00815,0.88581,0.00428,0.43686,0.98957,0.74704,0.35752,0.50656,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System 75293,SRR25598376,SRX21326028,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R1,3124R1,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F3-1_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L001_R1_001.fastq.gz 3124F3-1_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L001_R2_001.fastq.gz,fastq fastq,24948540624.0,297006436.0,3124F3 1 220322 A01563 0038 AHY3YHDRXY CCCACCACAA AAGCGGAGGT L001 R1 001.fastq.gz,0:28 1:56,A:7193047366;C:5189304192;G:5248299831;T:7317170808;N:718427,28,56,,,7193047366,5189304192,5248299831,7317170808,718427,SRX21326028,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00769,0.89098,0.00387,0.42984,0.99038,0.74878,0.30434,0.49663,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System 75294,SRR25598377,SRX21326027,SRS18572180,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3065R,,breed:wildtype|age:8 mpf|dev stage:adult|collection date:2022 01 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3065R,3065R,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3065F1-1_220118_NB501735_0823_AH3HHLBGXL_GTAACATG-NoIndex_L000_R1_001.fastq.gz 3065F1-1_220118_NB501735_0823_AH3HHLBGXL_GTAACATG-NoIndex_L000_R2_001.fastq.gz,fastq fastq,35548236948.0,423193297.0,3065F1 1 220118 NB501735 0823 AH3HHLBGXL GTAACATG NoIndex L000 R1 001.fastq.gz,0:28 1:56,A:10224422089;C:7414175917;G:7794098189;T:10109777968;N:5762785,28,56,,,10224422089,7414175917,7794098189,10109777968,5762785,SRX21326027,SRS18572180,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00913,0.90845,0.00399,0.3776,0.99024,0.75455,0.32653,0.50632,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System