metadata: run_metadata: 17 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue

17 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
26493	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.			Rtf1MO single cell Multiome GEX 11 12 somite stage	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	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729		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		0.43479		0.76881		0.57534		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26494	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.			Control single cell Multiome GEX 11 12 somite stage	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	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729		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		0.37406		0.75481		0.57841		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26495	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.			Rtf1MO single cell Multiome GEX 11 12 somite stage	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	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729		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	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26496	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.			Control single cell Multiome GEX 11 12 somite stage	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	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729		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	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26497	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.			Rtf1MO single cell Multiome GEX 11 12 somite stage	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	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729		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		0.43202		0.7725		0.56861		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
26498	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.			Control single cell Multiome GEX 11 12 somite stage	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	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459729		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		0.37342		0.75668		0.45872		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2023-09-12	Segmentation	Embryo	Whole Organism	All anatomical structures
31963	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 t…			7b	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	scRNA seq of whole zebrafish larvae	7b	7b	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			18993507272	15386021146	15634918803	17652028346	22462612	SRX24395271	SRS21150709	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31964	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 t…			7a	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	scRNA seq of whole zebrafish larvae	7a	7a	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			22179167002	18012103520	18280647088	20603509593	26357051	SRX24395270	SRS21150708	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31965	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 t…			6b	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	scRNA seq of whole zebrafish larvae	6b	6b	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			19762887143	15877063714	15450633995	18460750107	16407724	SRX24395269	SRS21150710	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31966	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 t…			6a	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	scRNA seq of whole zebrafish larvae	6a	6a	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		6a_concatenated_R1.fastq.gz 6a_concatenated_R2.fastq.gz	fastq fastq	69092868528.0	535603632.0	6a concatenated R1.fastq.gz												SRX24395268	SRS21150711	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31967	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 t…			5c	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	scRNA seq of whole zebrafish larvae	5c	5c	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			12472930469	9646780605	9513754487	11098062350	6622041	SRX24395267	SRS21150707	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31968	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 t…			4b	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	scRNA seq of whole zebrafish larvae	4b	4b	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			19966236558	16224236063	16033442126	18882486499	62148748	SRX24395266	SRS21150706	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31969	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 t…			4a	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	scRNA seq of whole zebrafish larvae	4a	4a	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			19390338294	15653316754	15467157018	18205511068	15905512	SRX24395265	SRS21150705	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31970	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 t…			3b	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	scRNA seq of whole zebrafish larvae	3b	3b	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		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			18187699043	14602482735	14672400468	17481975446	22213844	SRX24395264	SRS21150704	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
31971	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 t…			3a	strain:ABC\|dev stage:3 dpf\|collection date:2020 10\|geo loc name:USA: Oregon\|sex:N/A\|tissue:whole larvae\|treatment:replicate A\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish larvae	3a	3a	10X Chromium	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662		3a_concatenated_R1.fastq.gz 3a_concatenated_R2.fastq.gz	fastq fastq	68966162664.0	534621416.0	3a concatenated R1.fastq.gz	0:28 1:101	A:19232364475;C:15520559864;G:15732756322;T:18456921265;N:23560738	28	101			19232364475	15520559864	15732756322	18456921265	23560738	SRX24395263	SRS21150703	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures
60657	60657	SRR15046102	SRX11356738	SRS9403587	SRP278034	PRJNA657343	Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development	PRJNA657343	Other	Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.	scRNAseq	scRNAseq Satb2 MUT 14som	scRNAseq Satb2 MUT 14som	strain:Satb2 Mutant\|age:14 somite\|dev stage:14 somite\|sex:not applicable\|tissue:whole embryo\|replicate:replicate = Biological replicate1\|BioSampleModel:Model organism or animal	Satb2 mutants single cell RNAseq	Satb2 MUT 14ss scRNAseq	Satb2 MUT 14ss scRNAseq	according 10X three primemRNA seq V3.2 protocol	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	NextSeq 550	SRP278034	loader:fastq load.py			23142978710.0	177123922.0	scRNAseq Satb2 MUT 14som I1.fastq.gz	0:8 1:30 2:92.66	A:4753575949;C:3375880000;G:3751151628;T:4500225651;N:31436446	8	30	92		4753575949	3375880000	3751151628	4500225651	31436446	SRX11356738	SRS9403587	SRA1254741	IISER-PUNE\|biology	IISER-PUNE	1	0.80351		0.14479		0.79695		0.55274		101		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	India	2021-07-13	Segmentation	Embryo	Whole Organism	All anatomical structures
60658	60658	SRR15046103	SRX11356737	SRS9403586	SRP278034	PRJNA657343	Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development	PRJNA657343	Other	Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.	scRNAseq	scRNAseq WT 14som	scRNAseq WT 14som	strain:Wild type sibling\|age:14 somite\|dev stage:14 somite\|sex:not applicable\|tissue:whole embryo\|replicate:replicate = Biological replicate1\|BioSampleModel:Model organism or animal	Satb2 siblings single cell RNAseq	WT sibs 14ss scRNAseq	WT sibs 14ss scRNAseq	according 10X three primemRNA seq V3.2 protocol	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	NextSeq 550	SRP278034	loader:fastq load.py\|options: mixedDeflines maxErrorCount=0			27847103625.0	200338875.0	scRNAseq WT 14som I1.fastq.gz	0:8 1:30 2:101	A:5948912529;C:4138132473;G:4588280753;T:5527087357;N:31813263	8	30	101		5948912529	4138132473	4588280753	5527087357	31813263	SRX11356737	SRS9403586	SRA1254741	IISER-PUNE\|biology	IISER-PUNE	1	0.92298		0.15133		0.78906		0.54933		101		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	India	2021-07-13	Segmentation	Embryo	Whole Organism	All anatomical structures

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