{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"Oligo-dT\", experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation = \"Whole Organism\"", "rows": [[26493, "SRR26044865", "SRX21761777", "SRS18868295", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "Rtf1MO single cell Multiome GEX 11 12 somite stage", null, "strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:rtf1|assay:GEX|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq", "GEX MO", "GEX MO", "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459729", null, null, "MO-3GEX_S2_L002_R2_001.fastq.gz MO-3GEX_S2_L002_R1_001.fastq.gz MO-3GEX_S2_L002_I2_001.fastq.gz MO-3GEX_S2_L002_I1_001.fastq.gz MO-3GEX_S2_L001_R2_001.fastq.gz MO-3GEX_S2_L001_R1_001.fastq.gz MO-3GEX_S2_L001_I2_001.fastq.gz MO-3GEX_S2_L001_I1_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 50770012872.0, 367898644.0, "MO 3GEX S2 L001 I1 001.fastq.gz", "0:10 1:10 2:28 3:90", "A:10123747774;C:6493264924;G:7104700568;T:9387645989;N:1518705", 10, 10, 28, 90, 10123747774, 6493264924, 7104700568, 9387645989, 1518705, "SRX21761777", "SRS18868295", "SRA1710715", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.87322, null, 0.43479, null, 0.76881, null, 0.57534, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-09-12", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [26494, "SRR26044866", "SRX21761776", "SRS18868294", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "Control single cell Multiome GEX 11 12 somite stage", null, "strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:uninjected|assay:GEX|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq", "GEX WT", "GEX WT", "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459729", null, null, "WT-3GEX_S1_L001_I1_001.fastq.gz WT-3GEX_S1_L001_I2_001.fastq.gz WT-3GEX_S1_L001_R1_001.fastq.gz WT-3GEX_S1_L001_R2_001.fastq.gz WT-3GEX_S1_L002_I1_001.fastq.gz WT-3GEX_S1_L002_I2_001.fastq.gz WT-3GEX_S1_L002_R1_001.fastq.gz WT-3GEX_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 54878873586.0, 397672997.0, "WT 3GEX S1 L001 I1 001.fastq.gz", "0:10 1:10 2:28 3:90", "A:10837179080;C:7155333415;G:7765967855;T:10030437304;N:1652076", 10, 10, 28, 90, 10837179080, 7155333415, 7765967855, 10030437304, 1652076, "SRX21761776", "SRS18868294", "SRA1710715", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.89445, null, 0.37406, null, 0.75481, null, 0.57841, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-09-12", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [26495, "SRR26044766", "SRX21761676", "SRS18868295", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "Rtf1MO single cell Multiome GEX 11 12 somite stage", null, "strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:rtf1|assay:GEX|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq", "GEX MO", "GEX MO", "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459729", null, null, "MO_3GEX_S2_L004_R2_001.fastq.gz MO_3GEX_S2_L004_R1_001.fastq.gz MO_3GEX_S2_L004_I2_001.fastq.gz MO_3GEX_S2_L004_I1_001.fastq.gz MO_3GEX_S2_L003_R2_001.fastq.gz MO_3GEX_S2_L003_R1_001.fastq.gz MO_3GEX_S2_L003_I2_001.fastq.gz MO_3GEX_S2_L003_I1_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 2914080840.0, 13245822.0, "MO 3GEX S2 L003 I1 001.fastq.gz", "0:10 1:10 2:100 3:100", "A:726829083;C:402485666;G:452882760;T:1066890018;N:76873", 10, 10, 100, 100, 726829083, 402485666, 452882760, 1066890018, 76873, "SRX21761676", "SRS18868295", "SRA1710703", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 2, 0.22802, 0.87048, 0.10701, 0.42845, 0.95595, 0.77015, 0.60757, 0.57362, 100, 100, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-09-12", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [26496, "SRR26044767", "SRX21761675", "SRS18868294", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "Control single cell Multiome GEX 11 12 somite stage", null, "strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:uninjected|assay:GEX|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq", "GEX WT", "GEX WT", "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459729", null, null, "WT_3GEX_S1_L004_R2_001.fastq.gz WT_3GEX_S1_L004_R1_001.fastq.gz WT_3GEX_S1_L004_I2_001.fastq.gz WT_3GEX_S1_L004_I1_001.fastq.gz WT_3GEX_S1_L003_R2_001.fastq.gz WT_3GEX_S1_L003_R1_001.fastq.gz WT_3GEX_S1_L003_I2_001.fastq.gz WT_3GEX_S1_L003_I1_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 4986906540.0, 22667757.0, "WT 3GEX S1 L003 I1 001.fastq.gz", "0:10 1:10 2:100 3:100", "A:1227427708;C:695004251;G:785531191;T:1825414315;N:173935", 10, 10, 100, 100, 1227427708, 695004251, 785531191, 1825414315, 173935, "SRX21761675", "SRS18868294", "SRA1710703", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 2, 0.21872, 0.89321, 0.09696, 0.36976, 0.9558, 0.75639, 0.62213, 0.46544, 100, 100, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-09-12", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [26497, "SRR26044613", "SRX21761588", "SRS18868295", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "Rtf1MO single cell Multiome GEX 11 12 somite stage", null, "strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:rtf1|assay:GEX|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq", "GEX MO", "GEX MO", "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459729", null, null, "MO_3GEX_S2_L002_R2_001.fastq.gz MO_3GEX_S2_L002_R1_001.fastq.gz MO_3GEX_S2_L002_I2_001.fastq.gz MO_3GEX_S2_L002_I1_001.fastq.gz MO_3GEX_S2_L001_R2_001.fastq.gz MO_3GEX_S2_L001_R1_001.fastq.gz MO_3GEX_S2_L001_I2_001.fastq.gz MO_3GEX_S2_L001_I1_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 21527638854.0, 155997383.0, "MO 3GEX S2 L001 I1 001.fastq.gz", "0:10 1:10 2:28 3:90", "A:4285470476;C:2755587559;G:3034249420;T:3964137056;N:319959", 10, 10, 28, 90, 4285470476, 2755587559, 3034249420, 3964137056, 319959, "SRX21761588", "SRS18868295", "SRA1710658", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.87277, null, 0.43202, null, 0.7725, null, 0.56861, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-09-12", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [26498, "SRR26044614", "SRX21761587", "SRS18868294", "SRP459729", "PRJNA1015262", "Rtf1 dependent transcriptional pausing regulates cardiogenesis", "PRJNA1015262", "Other", "During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.", null, null, null, null, "Control single cell Multiome GEX 11 12 somite stage", null, "strain:AB|age:11 12 somite stage|collection date:2021 03 10|geo loc name:USA:California Los Angeles|sex:n/a|tissue:whole embryo|morpholino:uninjected|assay:GEX|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10x single cell multiome analysis of 11 12 somite stage zebrafish embryos: single cell RNA seq", "GEX WT", "GEX WT", "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459729", null, null, "WT_3GEX_S1_L001_I1_001.fastq.gz WT_3GEX_S1_L001_I2_001.fastq.gz WT_3GEX_S1_L001_R1_001.fastq.gz WT_3GEX_S1_L001_R2_001.fastq.gz WT_3GEX_S1_L002_I1_001.fastq.gz WT_3GEX_S1_L002_I2_001.fastq.gz WT_3GEX_S1_L002_R1_001.fastq.gz WT_3GEX_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq", 24359922978.0, 176521181.0, "WT 3GEX S1 L001 I1 001.fastq.gz", "0:10 1:10 2:28 3:90", "A:4802729436;C:3179460152;G:3468651943;T:4435697892;N:366867", 10, 10, 28, 90, 4802729436, 3179460152, 3468651943, 4435697892, 366867, "SRX21761587", "SRS18868294", "SRA1710658", "University of California, Los Angeles|Molecular, Cell, and Developmental Biology", "University of California, Los Angeles", 1, 0.89475, null, 0.37342, null, 0.75668, null, 0.45872, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-09-12", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [31963, "SRR28832522", "SRX24395271", "SRS21150709", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "7b", null, "strain:ABC|dev stage:7 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "7b", "7b", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "7b_concatenated_R1.fastq.gz 7b_concatenated_R2.fastq.gz", "fastq fastq", 67688938179.0, 524720451.0, "7b concatenated R1.fastq.gz", "0:28 1:101", "A:18993507272;C:15386021146;G:15634918803;T:17652028346;N:22462612", 28, 101, null, null, 18993507272, 15386021146, 15634918803, 17652028346, 22462612, "SRX24395271", "SRS21150709", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31964, "SRR28832523", "SRX24395270", "SRS21150708", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "7a", null, "strain:ABC|dev stage:7 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "7a", "7a", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "7a_concatenated_R1.fastq.gz 7a_concatenated_R2.fastq.gz", "fastq fastq", 79101784254.0, 613192126.0, "7a concatenated R1.fastq.gz", "0:28 1:101", "A:22179167002;C:18012103520;G:18280647088;T:20603509593;N:26357051", 28, 101, null, null, 22179167002, 18012103520, 18280647088, 20603509593, 26357051, "SRX24395270", "SRS21150708", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31965, "SRR28832524", "SRX24395269", "SRS21150710", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "6b", null, "strain:ABC|dev stage:6 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "6b", "6b", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "6b_concatenated_R1.fastq.gz 6b_concatenated_R2.fastq.gz", "fastq fastq", 69567742683.0, 539284827.0, "6b concatenated R1.fastq.gz", "0:28 1:101", "A:19762887143;C:15877063714;G:15450633995;T:18460750107;N:16407724", 28, 101, null, null, 19762887143, 15877063714, 15450633995, 18460750107, 16407724, "SRX24395269", "SRS21150710", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31966, "SRR28832525", "SRX24395268", "SRS21150711", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "6a", null, "strain:ABC|dev stage:6 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "6a", "6a", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "6a_concatenated_R1.fastq.gz 6a_concatenated_R2.fastq.gz", "fastq fastq", 69092868528.0, 535603632.0, "6a concatenated R1.fastq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX24395268", "SRS21150711", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31967, "SRR28832526", "SRX24395267", "SRS21150707", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "5c", null, "strain:ABC|dev stage:5 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "5c", "5c", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "5c_concatenated_R1.fastq.gz 5c_concatenated_R2.fastq.gz", "fastq fastq", 42738149952.0, 331303488.0, "5c concatenated R1.fastq.gz", "0:28 1:101", "A:12472930469;C:9646780605;G:9513754487;T:11098062350;N:6622041", 28, 101, null, null, 12472930469, 9646780605, 9513754487, 11098062350, 6622041, "SRX24395267", "SRS21150707", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31968, "SRR28832527", "SRX24395266", "SRS21150706", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "4b", null, "strain:ABC|dev stage:4 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "4b", "4b", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "4b_concatenated_R1.fastq.gz 4b_concatenated_R2.fastq.gz", "fastq fastq", 71168549994.0, 551694186.0, "4b concatenated R1.fastq.gz", "0:28 1:101", "A:19966236558;C:16224236063;G:16033442126;T:18882486499;N:62148748", 28, 101, null, null, 19966236558, 16224236063, 16033442126, 18882486499, 62148748, "SRX24395266", "SRS21150706", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31969, "SRR28832528", "SRX24395265", "SRS21150705", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "4a", null, "strain:ABC|dev stage:4 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "4a", "4a", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "4a_concatenated_R1.fastq.gz 4a_concatenated_R2.fastq.gz", "fastq fastq", 68732228646.0, 532807974.0, "4a concatenated R1.fastq.gz", "0:28 1:101", "A:19390338294;C:15653316754;G:15467157018;T:18205511068;N:15905512", 28, 101, null, null, 19390338294, 15653316754, 15467157018, 18205511068, 15905512, "SRX24395265", "SRS21150705", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31970, "SRR28832529", "SRX24395264", "SRS21150704", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. Our finding that the lens specific zebrafish alpha Ba crystallin plays the leading role in preventing age related cataract adds a new twist to our understanding of vertebrate lens evolution.", null, null, null, null, "3b", null, "strain:ABC|dev stage:3 dpf|collection date:2020 10|geo loc name:USA: Oregon|sex:N/A|tissue:whole larvae|treatment:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish larvae", "3b", "3b", "10X Chromium", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP504662", null, null, "3b_concatenated_R1.fastq.gz 3b_concatenated_R2.fastq.gz", "fastq fastq", 64966771536.0, 503618384.0, "3b concatenated R1.fastq.gz", "0:28 1:101", "A:18187699043;C:14602482735;G:14672400468;T:17481975446;N:22213844", 28, 101, null, null, 18187699043, 14602482735, 14672400468, 17481975446, 22213844, "SRX24395264", "SRS21150704", "SRA1854140", "University of Oregon|Institute of Neuroscience", "University of Oregon", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31971, "SRR28832530", "SRX24395263", "SRS21150703", "SRP504662", "PRJNA1105232", "Loss of alpha Ba crystallin  but not alpha A crystallin  increases age related cataract in the zebrafish lens", "PRJNA1105232", "Other", "The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens  possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins  alpha A  and alpha B crystallin  and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly  while zebrafish express one lens specific alpha A crystallin gene cryaa  they express two alpha B crystallin genes  with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly  unlike mouse knockout models  we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf  with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively  and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development  while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish  showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins  or in the abundant beta B1 crystallin. Overall  these findings indicate an ontogenetic shift in the functional importance of individual alpha crystallins during zebrafish lens development. 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