metadata: run_metadata: 58 rows where experiment.library_selection = "cDNA", technology = "generic-scrnaseq-only" and tissue

58 rows where experiment.library_selection = "cDNA", technology = "generic-scrnaseq-only" 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	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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
25324	25324	SRR25820349	SRX21542119	SRS18751470	SRP457651	PRJNA1010830	Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis	GSE241971	Other	hand2 reporter expressing cardiac cells fail to migrate to the midline. To investigate the underlying molecular changes we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD / and hand2 FLD+/? sibling embryos respectively. Furthermore hand2 is broadly expressed within the LPM which gives rise to various cell lineages and tissues including the cardiovascular system blood kidneys mesothelium and limb connective tissue. To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf hand2 FLD+/? Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD / sibling embryos. ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with myl7:GFP cells		pubmed:39658721	MUT replicate1 scRNA	GSM7746945	source name:whole embryo\|tissue:whole embryo\|cell type:hand2 reporter expressing single cells\|genotype:hand2 mutants\|geo loc name:missing\|collection date:missing	MUT replicate1 scRNA	demultiplexing star solo mapping: ' soloType CB UMI Simple soloBarcodeReadLength 0 soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix barcodes and genes	whole embryo		10xGenomics	tissue:whole embryo\|cell type:hand2 reporter expressing single cells\|genotype:hand2 mutants	GSM7746945	GSM7746945: MUT replicate1 scRNA; Danio rerio; RNA Seq	GSM7746945 r1	GSM7746945	1	10xGenomics	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP457651		Yanli_10x_Mut_24hpf_R2.fastq.gz Yanli_10x_Mut_24hpf_R1.fastq.gz	fastq fastq	12703207777.0	159786155.0	GSM7746945 r1	0:28 1:51.50	A:3417159154;C:2758515982;G:2823785724;T:3638099229;N:65647688	28	51			3417159154	2758515982	2823785724	3638099229	65647688	SRX21542119	SRS18751470	SRA1702565	Max Planck Institute for Heart and Lung Research	Max Planck Institute for Heart and Lung Research	2	0.00189	0.93843	0.0006	0.12822	0.99571	0.781	0.38429	0.49855	28	52	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	Germany	2023-08-30	Undetermined	Embryo	Whole Organism	All anatomical structures
25325	25325	SRR25820350	SRX21542118	SRS18751469	SRP457651	PRJNA1010830	Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis	GSE241971	Other	hand2 reporter expressing cardiac cells fail to migrate to the midline. To investigate the underlying molecular changes we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD / and hand2 FLD+/? sibling embryos respectively. Furthermore hand2 is broadly expressed within the LPM which gives rise to various cell lineages and tissues including the cardiovascular system blood kidneys mesothelium and limb connective tissue. To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf hand2 FLD+/? Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD / sibling embryos. ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with myl7:GFP cells		pubmed:39658721	WT replicate 1 scRNA	GSM7746944	source name:whole embryo\|tissue:whole embryo\|cell type:hand2 reporter expressing single cells\|genotype:WT\|geo loc name:missing\|collection date:missing	WT replicate 1 scRNA	demultiplexing star solo mapping: ' soloType CB UMI Simple soloBarcodeReadLength 0 soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix barcodes and genes	whole embryo		10xGenomics	tissue:whole embryo\|cell type:hand2 reporter expressing single cells\|genotype:WT	GSM7746944	GSM7746944: WT replicate 1 scRNA; Danio rerio; RNA Seq	GSM7746944 r1	GSM7746944	1	10xGenomics	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP457651		Yanli_10x_WT_24hpf_R2.fastq.gz Yanli_10x_WT_24hpf_R1.fastq.gz	fastq fastq	9691697994.0	121912639.0	GSM7746944 r1	0:28 1:51.50	A:2617434834;C:2102210357;G:2159290265;T:2762773221;N:49989317	28	51			2617434834	2102210357	2159290265	2762773221	49989317	SRX21542118	SRS18751469	SRA1702565	Max Planck Institute for Heart and Lung Research	Max Planck Institute for Heart and Lung Research	2	0.00175	0.93872	0.00057	0.12715	0.99584	0.78713	0.40888	0.504	28	52	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	Germany	2023-08-30	Undetermined	Embryo	Whole Organism	All anatomical structures
28611	28611	SRR26471890	SRX22175831	SRS19233331	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb mut eos 2	GSM7854238	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb mut eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP	GSM7854238	GSM7854238: cebpb mut eos 2; Danio rerio; RNA Seq	GSM7854238 r1	GSM7854238	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	F2_1.fq.gz F2_2.fq.gz	fastq fastq	6304806000.0	21016020.0	GSM7854238 r1	0:150 1:150	A:1797551316;C:1332146220;G:1348919312;T:1826125402;N:63750	150	150			1797551316	1332146220	1348919312	1826125402	63750	SRX22175831	SRS19233331	SRA1737851	South China University of Technology	South China University of Technology	2	0.90391	0.90473	0.3135	0.31222	0.83753	0.83613	0.53444	0.53443	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28612	28612	SRR26471891	SRX22175830	SRS19233328	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb wt eos 1	GSM7854239	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb wt eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854239	GSM7854239: cebpb wt eos 1; Danio rerio; RNA Seq	GSM7854239 r1	GSM7854239	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	Z1_1.fq.gz Z1_2.fq.gz	fastq fastq	6180805800.0	20602686.0	GSM7854239 r1	0:150 1:150	A:1699796929;C:1374020384;G:1377922189;T:1729003691;N:62607	150	150			1699796929	1374020384	1377922189	1729003691	62607	SRX22175830	SRS19233328	SRA1737851	South China University of Technology	South China University of Technology	2	0.91982	0.9224	0.18189	0.18148	0.82814	0.82672	0.51271	0.5152	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28613	28613	SRR26471892	SRX22175829	SRS19233330	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb wt eos 2	GSM7854240	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb wt eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854240	GSM7854240: cebpb wt eos 2; Danio rerio; RNA Seq	GSM7854240 r1	GSM7854240	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	Z2_1.fq.gz Z2_2.fq.gz	fastq fastq	6693470100.0	22311567.0	GSM7854240 r1	0:150 1:150	A:1840742978;C:1484923084;G:1499378237;T:1868364754;N:61047	150	150			1840742978	1484923084	1499378237	1868364754	61047	SRX22175829	SRS19233330	SRA1737851	South China University of Technology	South China University of Technology	2	0.92056	0.92353	0.18668	0.18721	0.82771	0.82696	0.53034	0.52277	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28614	28614	SRR26471893	SRX22175828	SRS19233332	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb mut eos 1	GSM7854237	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb mut eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP	GSM7854237	GSM7854237: cebpb mut eos 1; Danio rerio; RNA Seq	GSM7854237 r1	GSM7854237	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	F1_1.fq.gz F1_2.fq.gz	fastq fastq	7774783500.0	25915945.0	GSM7854237 r1	0:150 1:150	A:2205128515;C:1660071767;G:1677499789;T:2232048253;N:35176	150	150			2205128515	1660071767	1677499789	2232048253	35176	SRX22175828	SRS19233332	SRA1737851	South China University of Technology	South China University of Technology	2	0.90668	0.90886	0.34302	0.34395	0.81943	0.81937	0.5348	0.54523	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28615	28615	SRR26471894	SRX22175827	SRS19233329	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 wt eos 2	GSM7854236	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 wt eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854236	GSM7854236: cebp1 wt eos 2; Danio rerio; RNA Seq	GSM7854236 r1	GSM7854236	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	W2_1.fq.gz W2_2.fq.gz	fastq fastq	6478425300.0	21594751.0	GSM7854236 r1	0:150 1:150	A:2031706672;C:1135087913;G:1324534931;T:1987064653;N:31131	150	150			2031706672	1135087913	1324534931	1987064653	31131	SRX22175827	SRS19233329	SRA1737851	South China University of Technology	South China University of Technology	2	0.74912	0.74531	0.50454	0.49737	0.79255	0.78539	0.63484	0.64052	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28616	28616	SRR26471895	SRX22175826	SRS19233326	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 wt eos 1	GSM7854235	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 wt eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854235	GSM7854235: cebp1 wt eos 1; Danio rerio; RNA Seq	GSM7854235 r1	GSM7854235	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	W1_2.fq.gz W1_1.fq.gz	fastq fastq	6194437200.0	20648124.0	GSM7854235 r1	0:150 1:150	A:1953684038;C:1067667551;G:1247879965;T:1925172690;N:32956	150	150			1953684038	1067667551	1247879965	1925172690	32956	SRX22175826	SRS19233326	SRA1737851	South China University of Technology	South China University of Technology	2	0.76007	0.76295	0.54521	0.54298	0.78244	0.77281	0.62357	0.62562	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28617	28617	SRR26471896	SRX22175825	SRS19233327	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 mut eos 2	GSM7854234	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 mut eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP	GSM7854234	GSM7854234: cebp1 mut eos 2; Danio rerio; RNA Seq	GSM7854234 r1	GSM7854234	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	M2_2.fq.gz M2_1.fq.gz	fastq fastq	6104680800.0	20348936.0	GSM7854234 r1	0:150 1:150	A:1804058925;C:1198439018;G:1326225576;T:1775930488;N:26793	150	150			1804058925	1198439018	1326225576	1775930488	26793	SRX22175825	SRS19233327	SRA1737851	South China University of Technology	South China University of Technology	2	0.8123	0.81465	0.42735	0.42341	0.78171	0.77567	0.46764	0.65485	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28618	28618	SRR26471897	SRX22175824	SRS19233325	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 mut eos 1	GSM7854233	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 mut eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP	GSM7854233	GSM7854233: cebp1 mut eos 1; Danio rerio; RNA Seq	GSM7854233 r1	GSM7854233	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	M1_1.fq.gz M1_2.fq.gz	fastq fastq	6409092000.0	21363640.0	GSM7854233 r1	0:150 1:150	A:1887432519;C:1294546709;G:1354360945;T:1872720156;N:31671	150	150			1887432519	1294546709	1354360945	1872720156	31671	SRX22175824	SRS19233325	SRA1737851	South China University of Technology	South China University of Technology	2	0.84504	0.84611	0.39473	0.39207	0.76319	0.75767	0.63936	0.62743	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
73913	73913	SRR23284054	SRX19227385	SRS16633552	SRP420237	PRJNA929924	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]	GSE224113	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo 6hpf rep2	GSM7012036	source name:whole embryo\|tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:6hpf\|geo loc name:missing\|collection date:missing	zebrafish embryo 6hpf rep2	Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq	whole embryo	20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:6hpf	GSM7012036	GSM7012036: zebrafish embryo 6hpf rep2; Danio rerio; RNA Seq	GSM7012036 r1	GSM7012036	1	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP420237	loader:fastq load.py	nextseq_20220515_slam_120122_6hr_S20_R1_001.fastq.gz	fastq	1231038044.0	16197869.0	GSM7012036 r1	0:76	A:287858332;C:300689662;G:294179125;T:348288250;N:22675	76				287858332	300689662	294179125	348288250	22675	SRX19227385	SRS16633552	SRA1587567	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.91125		0.06969		0.75538		0.55355		76		B		usable mapping rate	illumina	nextseq	unknown	poly_a	ribozero	sc_generic	single_cell_generic	generic-scrnaseq-only	Israel	2023-01-31	Gastrula	Embryo	Whole Organism	All anatomical structures
73914	73914	SRR23284055	SRX19227384	SRS16633551	SRP420237	PRJNA929924	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]	GSE224113	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo 1hpf rep2	GSM7012035	source name:whole embryo\|tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:1hpf\|geo loc name:missing\|collection date:missing	zebrafish embryo 1hpf rep2	Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq	whole embryo	20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:1hpf	GSM7012035	GSM7012035: zebrafish embryo 1hpf rep2; Danio rerio; RNA Seq	GSM7012035 r1	GSM7012035	1	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP420237	loader:fastq load.py	nextseq_20220515_slam_120122_1hr_S19_R1_001.fastq.gz	fastq	988543704.0	13007154.0	GSM7012035 r1	0:76	A:237897735;C:241764496;G:233504938;T:275357752;N:18783	76				237897735	241764496	233504938	275357752	18783	SRX19227384	SRS16633551	SRA1587567	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.93827		0.03581		0.78027		0.53364		76		B		usable mapping rate	illumina	nextseq	unknown	poly_a	ribozero	sc_generic	single_cell_generic	generic-scrnaseq-only	Israel	2023-01-31	Cleavage	Embryo	Whole Organism	All anatomical structures
73915	73915	SRR23284056	SRX19227383	SRS16633550	SRP420237	PRJNA929924	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]	GSE224113	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo 6hpf rep1	GSM7012034	source name:whole embryo\|tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:6hpf\|geo loc name:missing\|collection date:missing	zebrafish embryo 6hpf rep1	Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq	whole embryo	20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:6hpf	GSM7012034	GSM7012034: zebrafish embryo 6hpf rep1; Danio rerio; RNA Seq	GSM7012034 r1	GSM7012034	1	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP420237	loader:fastq load.py	novaseq_20220630_slam_120122_6h_1.fastq.gz novaseq_20220630_slam_120122_6h_2.fastq.gz	fastq fastq	7578082116.0	37515258.0	GSM7012034 r1	0:101 1:101	A:1938942537;C:1836634013;G:1866966085;T:1935520946;N:18535	101	101			1938942537	1836634013	1866966085	1935520946	18535	SRX19227383	SRS16633550	SRA1587567	Hebrew University of Jerusalem	Hebrew University of Jerusalem	2	0.86852	0.87284	0.11981	0.11692	0.7571	0.75702	0.63941	0.63601	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	sc_generic	single_cell_generic	generic-scrnaseq-only	Israel	2023-01-31	Gastrula	Embryo	Whole Organism	All anatomical structures
73916	73916	SRR23284057	SRX19227382	SRS16633549	SRP420237	PRJNA929924	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]	GSE224113	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo 1hpf rep1	GSM7012033	source name:whole embryo\|tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:1hpf\|geo loc name:missing\|collection date:missing	zebrafish embryo 1hpf rep1	Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq	whole embryo	20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	tissue:whole embryo\|genotype:AB/TL\|treatment:4sU injection\|time:1hpf	GSM7012033	GSM7012033: zebrafish embryo 1hpf rep1; Danio rerio; RNA Seq	GSM7012033 r1	GSM7012033	1	Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP420237	loader:fastq load.py	novaseq_20220630_slam_120122_1h_1.fastq.gz novaseq_20220630_slam_120122_1h_2.fastq.gz	fastq fastq	7422864306.0	36746853.0	GSM7012033 r1	0:101 1:101	A:1927554601;C:1775023714;G:1801237102;T:1919030393;N:18496	101	101			1927554601	1775023714	1801237102	1919030393	18496	SRX19227382	SRS16633549	SRA1587567	Hebrew University of Jerusalem	Hebrew University of Jerusalem	2	0.91995	0.92316	0.05523	0.05324	0.7595	0.75897	0.57483	0.57891	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	ribozero	sc_generic	single_cell_generic	generic-scrnaseq-only	Israel	2023-01-31	Cleavage	Embryo	Whole Organism	All anatomical structures
74361	74361	SRR30639559	SRX26061375	SRS22630890	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR110	TDR110 30sinternew EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|collection date:2022 11 30\|geo loc name:USA: California San Francisco\|sex:not determined\|tissue:Whole embryo\|replicate:4\|BioSampleModel:Model organism or animal								TDR110	TDR110 30sinternew EKW NA none 10x	TDR110 30sinternew EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR110_30sinternew_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR110 30sinternew EKW NA none 10x S8 L001 I1 001.fastq.gz												SRX26061375		SRA1969971	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2024-09-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
74362	74362	SRR30639560	SRX26061374	SRS22630889	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR108	TDR108 30sinternew EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|collection date:2022 11 30\|geo loc name:USA: California San Francisco\|sex:not determined\|tissue:Whole embryo\|replicate:3\|BioSampleModel:Model organism or animal								TDR108	TDR108 30sinternew EKW NA none 10x	TDR108 30sinternew EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR108_30sinternew_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR108 30sinternew EKW NA none 10x S7 L001 I1 001.fastq.gz												SRX26061374		SRA1969971	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2024-09-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
74363	74363	SRR30639561	SRX26061373	SRS22630888	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR107	TDR107 30sinternew EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|collection date:2022 11 30\|geo loc name:USA: California San Francisco\|sex:not determined\|tissue:Whole embryo\|replicate:2\|BioSampleModel:Model organism or animal								TDR107	TDR107 30sinternew EKW NA none 10x	TDR107 30sinternew EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR107_30sinternew_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR107 30sinternew EKW NA none 10x S6 L001 I1 001.fastq.gz												SRX26061373		SRA1969971	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2024-09-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
74364	74364	SRR30639562	SRX26061372	SRS22630887	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR106	TDR106 30sinternew EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|collection date:2022 11 30\|geo loc name:USA: California San Francisco\|sex:not determined\|tissue:Whole embryo\|replicate:1\|BioSampleModel:Model organism or animal								TDR106	TDR106 30sinternew EKW NA none 10x	TDR106 30sinternew EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR106_30sinternew_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR106 30sinternew EKW NA none 10x S5 L001 I1 001.fastq.gz												SRX26061372		SRA1969971	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2024-09-11	Pharyngula	Embryo	Whole Organism	All anatomical structures
74365	74365	SRR23691708	SRX19554131	SRS16938876	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR69	TDR69 3dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:3 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR69	TDR69 3dpf EKW NA none 10x	TDR69 3dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR69_3dpf_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	141857572788.0	1027953426.0	TDR69 3dpf EKW NA none 10x S7 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:28328864562;C:19239372522;G:21305538387;T:23641635703;N:397166	10	10	28	90	28328864562	19239372522	21305538387	23641635703	397166	SRX19554131	SRS16938876	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.88204		0.16198		0.75755		0.60319		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74366	74366	SRR23691680	SRX19554130	SRS16938877	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR68	TDR68 3dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:3 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR68	TDR68 3dpf EKW NA none 10x	TDR68 3dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR68_3dpf_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	110769022074.0	802674073.0	TDR68 3dpf EKW NA none 10x S6 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:22289181655;C:15092942636;G:16399615434;T:18458614634;N:312211	10	10	28	90	22289181655	15092942636	16399615434	18458614634	312211	SRX19554130	SRS16938877	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.8863		0.13277		0.7763		0.63421		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74367	74367	SRR23691681	SRX19554129	SRS16938875	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR67	TDR67 3dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:3 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR67	TDR67 3dpf EKW NA none 10x	TDR67 3dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR67_3dpf_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	119516314086.0	866060247.0	TDR67 3dpf EKW NA none 10x S5 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:24193630011;C:16247091070;G:17646962144;T:19857399932;N:339073	10	10	28	90	24193630011	16247091070	17646962144	19857399932	339073	SRX19554129	SRS16938875	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.88156		0.15085		0.77735		0.65657		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74368	74368	SRR23691682	SRX19554128	SRS16938874	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR54	TDR54 5dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:5 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR54	TDR54 5dpf EKW NA none 10x	TDR54 5dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR54_5dpf_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	102943738698.0	745969121.0	TDR54 5dpf EKW NA none 10x S8 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:18441288819;C:15293958091;G:17147898256;T:16254015416;N:60308	10	10	28	90	18441288819	15293958091	17147898256	16254015416	60308	SRX19554128	SRS16938874	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.90349		0.2328		0.78865		0.64502		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74369	74369	SRR23691683	SRX19554127	SRS16938873	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR22	TDR22 10somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:14 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR22	TDR22 10somite EKW NA none 10x	TDR22 10somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR22_10somite_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR22 10somite EKW NA none 10x S4 L001 I1 001.fastq.gz												SRX19554127		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74370	74370	SRR23691685	SRX19554126	SRS16938872	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR52	TDR52 5dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:5 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR52	TDR52 5dpf EKW NA none 10x	TDR52 5dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR52_5dpf_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	101121414750.0	732763875.0	TDR52 5dpf EKW NA none 10x S6 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:18381382068;C:14949962451;G:16391823629;T:16225521055;N:59547	10	10	28	90	18381382068	14949962451	16391823629	16225521055	59547	SRX19554126	SRS16938872	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.92316		0.19197		0.77337		0.62427		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74371	74371	SRR23691702	SRX19554125	SRS16938871	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR24	TDR24 budstage EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR24	TDR24 budstage EKW NA none 10x	TDR24 budstage EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR24_budstage_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR24 budstage EKW NA none 10x S2 L001 I1 001.fastq.gz												SRX19554125		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Gastrula	Embryo	Whole Organism	All anatomical structures
74372	74372	SRR23691684	SRX19554124	SRS16938870	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR53	TDR53 5dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:5 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR53	TDR53 5dpf EKW NA none 10x	TDR53 5dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR53_5dpf_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	67168978188.0	486731726.0	TDR53 5dpf EKW NA none 10x S7 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:12286816007;C:9835631121;G:10821946765;T:10861420866;N:40581	10	10	28	90	12286816007	9835631121	10821946765	10861420866	40581	SRX19554124	SRS16938870	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.92074		0.21231		0.77488		0.65154		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74373	74373	SRR23691686	SRX19554123	SRS16938869	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR51	TDR51 5dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:5 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR51	TDR51 5dpf EKW NA none 10x	TDR51 5dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR51_5dpf_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	107234170842.0	777059209.0	TDR51 5dpf EKW NA none 10x S5 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:19755252329;C:15612604707;G:17171775681;T:17395631095;N:64998	10	10	28	90	19755252329	15612604707	17171775681	17395631095	64998	SRX19554123	SRS16938869	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.90333		0.21644		0.76706		0.65091		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74374	74374	SRR23691687	SRX19554122	SRS16938868	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR50	TDR50 2dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:2 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR50	TDR50 2dpf EKW NA none 10x	TDR50 2dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR50_2dpf_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L001_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	110075703450.0	797650025.0	TDR50 2dpf EKW NA none 10x S4 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:19338422691;C:16766252744;G:19693997103;T:15989765605;N:64107	10	10	28	90	19338422691	16766252744	19693997103	15989765605	64107	SRX19554122	SRS16938868	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.87838		0.18625		0.8355		0.58184		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Hatching	Embryo	Whole Organism	All anatomical structures
74375	74375	SRR23691717	SRX19554121	SRS16938867	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR41	TDR41 15somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:16 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR41	TDR41 15somite EKW NA none 10x	TDR41 15somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR41_15somite_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	93499956408.0	677535916.0	TDR41 15somite EKW NA none 10x S7 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:17289943134;C:13691132218;G:15290920650;T:14706171425;N:65013	10	10	28	90	17289943134	13691132218	15290920650	14706171425	65013	SRX19554121	SRS16938867	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.94201		0.12543		0.80129		0.52789		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74376	74376	SRR23691689	SRX19554120	SRS16938866	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR40	TDR40 15somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:16 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR40	TDR40 15somite EKW NA none 10x	TDR40 15somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR40_15somite_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	94772546316.0	686757582.0	TDR40 15somite EKW NA none 10x S6 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:17499834278;C:13832305488;G:15425748483;T:15050229511;N:64620	10	10	28	90	17499834278	13832305488	15425748483	15050229511	64620	SRX19554120	SRS16938866	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.93907		0.13477		0.79143		0.5485		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74377	74377	SRR23691690	SRX19554119	SRS16938865	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR39	TDR39 15somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:16 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR39	TDR39 15somite EKW NA none 10x	TDR39 15somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR39_15somite_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	134364525240.0	973655980.0	TDR39 15somite EKW NA none 10x S5 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:25028565859;C:19549118640;G:21889948945;T:21161311123;N:93633	10	10	28	90	25028565859	19549118640	21889948945	21161311123	93633	SRX19554119	SRS16938865	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.93786		0.13635		0.79817		0.5526		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74378	74378	SRR23691691	SRX19554118	SRS16938864	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR38	TDR38 5somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR38	TDR38 5somite EKW NA none 10x	TDR38 5somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR38_5somite_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L001_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	109163562504.0	791040308.0	TDR38 5somite EKW NA none 10x S4 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:20296889655;C:15295509612;G:16665411100;T:18935743224;N:74129	10	10	28	90	20296889655	15295509612	16665411100	18935743224	74129	SRX19554118	SRS16938864	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.94177		0.14801		0.79078		0.51715		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74379	74379	SRR23691692	SRX19554117	SRS16938863	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR37	TDR37 5somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR37	TDR37 5somite EKW NA none 10x	TDR37 5somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR37_5somite_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L001_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	86186871072.0	624542544.0	TDR37 5somite EKW NA none 10x S3 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:16098325109;C:11599595645;G:12688698356;T:15822148067;N:61783	10	10	28	90	16098325109	11599595645	12688698356	15822148067	61783	SRX19554117	SRS16938863	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.93181		0.14342		0.78293		0.50708		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74380	74380	SRR23691693	SRX19554116	SRS16938862	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR36	TDR36 5somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR36	TDR36 5somite EKW NA none 10x	TDR36 5somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR36_5somite_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L001_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	135123329832.0	979154564.0	TDR36 5somite EKW NA none 10x S2 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:25030401855;C:19108313489;G:21135503897;T:22849597141;N:94378	10	10	28	90	25030401855	19108313489	21135503897	22849597141	94378	SRX19554116	SRS16938862	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.93706		0.13959		0.79322		0.53064		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74381	74381	SRR23691715	SRX19554115	SRS16938861	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR43	TDR43 30somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR43	TDR43 30somite EKW NA none 10x	TDR43 30somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR43_30somite_EKW_NA_none_10x_S9_L001_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L001_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L001_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L001_R2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_R2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_R2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	149387152524.0	1082515598.0	TDR43 30somite EKW NA none 10x S9 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:27335818210;C:22229444114;G:24395538574;T:23465497486;N:105436	10	10	28	90	27335818210	22229444114	24395538574	23465497486	105436	SRX19554115	SRS16938861	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.93754		0.11997		0.79695		0.50775		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Pharyngula	Embryo	Whole Organism	All anatomical structures
74382	74382	SRR23691694	SRX19554114	SRS16938860	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR35	TDR35 5somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR35	TDR35 5somite EKW NA none 10x	TDR35 5somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR35_5somite_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L001_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR35 5somite EKW NA none 10x S1 L001 I1 001.fastq.gz												SRX19554114		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74383	74383	SRR23691695	SRX19554113	SRS16938859	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR30	TDR30 20somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:19 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR30	TDR30 20somite EKW NA none 10x	TDR30 20somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR30_20somite_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L001_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	126551285262.0	917038299.0	TDR30 20somite EKW NA none 10x S4 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:22992867453;C:19066092511;G:21900344853;T:18572896783;N:1245310	10	10	28	90	22992867453	19066092511	21900344853	18572896783	1245310	SRX19554113	SRS16938859	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.90514		0.17664		0.81921		0.58589		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74384	74384	SRR23691696	SRX19554112	SRS16938858	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR29	TDR29 20somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:19 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR29	TDR29 20somite EKW NA none 10x	TDR29 20somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR29_20somite_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L001_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR29 20somite EKW NA none 10x S3 L001 I1 001.fastq.gz												SRX19554112		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74385	74385	SRR23691697	SRX19554111	SRS16938857	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR27	TDR27 20somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:19 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR27	TDR27 20somite EKW NA none 10x	TDR27 20somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR27_20somite_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L001_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR27 20somite EKW NA none 10x S1 L001 I1 001.fastq.gz												SRX19554111		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74386	74386	SRR23691699	SRX19554110	SRS16938856	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR25	TDR25 budstage EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR25	TDR25 budstage EKW NA none 10x	TDR25 budstage EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR25_budstage_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR25 budstage EKW NA none 10x S3 L001 I1 001.fastq.gz												SRX19554110		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Gastrula	Embryo	Whole Organism	All anatomical structures
74387	74387	SRR23691701	SRX19554109	SRS16938855	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR23	TDR23 budstage EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR23	TDR23 budstage EKW NA none 10x	TDR23 budstage EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR23_budstage_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR23 budstage EKW NA none 10x S1 L001 I1 001.fastq.gz												SRX19554109		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Gastrula	Embryo	Whole Organism	All anatomical structures
74388	74388	SRR23691703	SRX19554108	SRS16938854	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR74	TDR74 10dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR74	TDR74 10dpf EKW NA none 10x	TDR74 10dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR74_10dpf_EKW_NA_none_10x_S12_L001_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L001_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L001_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L001_R2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_R2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_R2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	127541718162.0	924215349.0	TDR74 10dpf EKW NA none 10x S12 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:25488649266;C:17959072964;G:19518445217;T:20212853491;N:360472	10	10	28	90	25488649266	17959072964	19518445217	20212853491	360472	SRX19554108	SRS16938854	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.89605		0.11636		0.80359		0.67034		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74389	74389	SRR23691704	SRX19554107	SRS16938853	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR73	TDR73 10dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR73	TDR73 10dpf EKW NA none 10x	TDR73 10dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR73_10dpf_EKW_NA_none_10x_S11_L001_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L001_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L001_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L001_R2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_R2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_R2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	114302302866.0	828277557.0	TDR73 10dpf EKW NA none 10x S11 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:22714080081;C:16064432542;G:17485020946;T:18281123311;N:323250	10	10	28	90	22714080081	16064432542	17485020946	18281123311	323250	SRX19554107	SRS16938853	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.89363		0.11601		0.81264		0.66087		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74390	74390	SRR23691705	SRX19554106	SRS16938852	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR72	TDR72 10dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR72	TDR72 10dpf EKW NA none 10x	TDR72 10dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR72_10dpf_EKW_NA_none_10x_S10_L001_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L001_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L001_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L001_R2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_R2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_R2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	121568547690.0	880931505.0	TDR72 10dpf EKW NA none 10x S10 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:24679161080;C:16685502546;G:18726693111;T:19192140433;N:338280	10	10	28	90	24679161080	16685502546	18726693111	19192140433	338280	SRX19554106	SRS16938852	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.85476		0.12578		0.80906		0.6567		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74391	74391	SRR23691706	SRX19554105	SRS16938851	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR71	TDR71 10dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR71	TDR71 10dpf EKW NA none 10x	TDR71 10dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR71_10dpf_EKW_NA_none_10x_S9_L001_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L001_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L001_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L001_R2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_R2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_R2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	124544763606.0	902498287.0	TDR71 10dpf EKW NA none 10x S9 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:24670559612;C:17725900620;G:19044403365;T:19783628987;N:353246	10	10	28	90	24670559612	17725900620	19044403365	19783628987	353246	SRX19554105	SRS16938851	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.90676		0.09847		0.81475		0.67323		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74392	74392	SRR23691679	SRX19554104	SRS16938850	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR28	TDR28 20somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:19 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR28	TDR28 20somite EKW NA none 10x	TDR28 20somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR28_20somite_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L001_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR28 20somite EKW NA none 10x S2 L001 I1 001.fastq.gz												SRX19554104		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74393	74393	SRR23691707	SRX19554103	SRS16938849	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR70	TDR70 3dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:3 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR70	TDR70 3dpf EKW NA none 10x	TDR70 3dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR70_3dpf_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	105158760966.0	762020007.0	TDR70 3dpf EKW NA none 10x S8 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:21281448836;C:14331451262;G:15718459674;T:17250143686;N:297172	10	10	28	90	21281448836	14331451262	15718459674	17250143686	297172	SRX19554103	SRS16938849	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.87781		0.14577		0.77595		0.64139		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Larval	Larval	Whole Organism	All anatomical structures
74394	74394	SRR23691688	SRX19554102	SRS16938848	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR49	TDR49 2dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:2 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR49	TDR49 2dpf EKW NA none 10x	TDR49 2dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR49_2dpf_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L001_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	118537620432.0	858968264.0	TDR49 2dpf EKW NA none 10x S3 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:19359775172;C:19118553633;G:22580874113;T:16247869796;N:71046	10	10	28	90	19359775172	19118553633	22580874113	16247869796	71046	SRX19554102	SRS16938848	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.86228		0.22633		0.87436		0.68374		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Hatching	Embryo	Whole Organism	All anatomical structures
74395	74395	SRR23691709	SRX19554101	SRS16938847	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR48	TDR48 2dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:2 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR48	TDR48 2dpf EKW NA none 10x	TDR48 2dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR48_2dpf_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L001_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	130790722266.0	947758857.0	TDR48 2dpf EKW NA none 10x S2 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:22786070358;C:19996387148;G:23390030207;T:19125732270;N:77147	10	10	28	90	22786070358	19996387148	23390030207	19125732270	77147	SRX19554101	SRS16938847	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.86692		0.1987		0.82856		0.62968		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Hatching	Embryo	Whole Organism	All anatomical structures
74396	74396	SRR23691710	SRX19554100	SRS16938845	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR47	TDR47 2dpf EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:2 dpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR47	TDR47 2dpf EKW NA none 10x	TDR47 2dpf EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR47_2dpf_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L001_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	131472152880.0	952696760.0	TDR47 2dpf EKW NA none 10x S1 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:23266007781;C:19700328945;G:22763807680;T:20012485432;N:78562	10	10	28	90	23266007781	19700328945	22763807680	20012485432	78562	SRX19554100	SRS16938845	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.88128		0.22898		0.80665		0.64263		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Hatching	Embryo	Whole Organism	All anatomical structures
74397	74397	SRR23691711	SRX19554099	SRS16938846	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR46	TDR46 30somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR46	TDR46 30somite EKW NA none 10x	TDR46 30somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR46_30somite_EKW_NA_none_10x_S12_L001_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L001_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L001_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L001_R2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_R2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_R2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	113538856782.0	822745339.0	TDR46 30somite EKW NA none 10x S12 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:21088382542;C:16482826983;G:18272838919;T:18202952478;N:79588	10	10	28	90	21088382542	16482826983	18272838919	18202952478	79588	SRX19554099	SRS16938846	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.92485		0.12469		0.78441		0.51979		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Pharyngula	Embryo	Whole Organism	All anatomical structures
74398	74398	SRR23691712	SRX19554098	SRS16938844	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR45	TDR45 30somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR45	TDR45 30somite EKW NA none 10x	TDR45 30somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR45_30somite_EKW_NA_none_10x_S11_L001_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L001_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L001_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L001_R2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_R2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_R2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	151741402440.0	1099575380.0	TDR45 30somite EKW NA none 10x S11 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:28305264381;C:22203945096;G:24554199279;T:23898269926;N:105518	10	10	28	90	28305264381	22203945096	24554199279	23898269926	105518	SRX19554098	SRS16938844	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.92131		0.13041		0.78409		0.52692		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Pharyngula	Embryo	Whole Organism	All anatomical structures
74399	74399	SRR23691713	SRX19554097	SRS16938843	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR44	TDR44 30somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR44	TDR44 30somite EKW NA none 10x	TDR44 30somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR44_30somite_EKW_NA_none_10x_S10_L001_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L001_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L001_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L001_R2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_R2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_R2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR44 30somite EKW NA none 10x S10 L001 I1 001.fastq.gz												SRX19554097		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Pharyngula	Embryo	Whole Organism	All anatomical structures
74400	74400	SRR23691714	SRX19554096	SRS16938842	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR21	TDR21 10somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:14 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep3\|BioSampleModel:Model organism or animal								TDR21	TDR21 10somite EKW NA none 10x	TDR21 10somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR21_10somite_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR21 10somite EKW NA none 10x S3 L001 I1 001.fastq.gz												SRX19554096		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74401	74401	SRR23691716	SRX19554095	SRS16938841	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR42	TDR42 15somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:16 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR42	TDR42 15somite EKW NA none 10x	TDR42 15somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR42_15somite_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	104417359968.0	756647536.0	TDR42 15somite EKW NA none 10x S8 L001 I1 001.fastq.gz	0:10 1:10 2:28 3:90	A:19133695070;C:15471236758;G:17206957805;T:16286315487;N:73120	10	10	28	90	19133695070	15471236758	17206957805	16286315487	73120	SRX19554095	SRS16938841	SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub	1	0.94293		0.12989		0.80614		0.55582		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-03	Segmentation	Embryo	Whole Organism	All anatomical structures
74402	74402	SRR23691700	SRX19554094	SRS16938840	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR26	TDR26 budstage EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:10 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep4\|BioSampleModel:Model organism or animal								TDR26	TDR26 budstage EKW NA none 10x	TDR26 budstage EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR26_budstage_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR26 budstage EKW NA none 10x S4 L001 I1 001.fastq.gz												SRX19554094		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Gastrula	Embryo	Whole Organism	All anatomical structures
74403	74403	SRR23691698	SRX19554093	SRS16938839	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR19	TDR19 10somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:14 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep2\|BioSampleModel:Model organism or animal								TDR19	TDR19 10somite EKW NA none 10x	TDR19 10somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR19_10somite_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR19 10somite EKW NA none 10x S2 L001 I1 001.fastq.gz												SRX19554093		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	Segmentation	Embryo	Whole Organism	All anatomical structures
74404	74404	SRR23691718	SRX19554092	SRS16939474	SRP425398	PRJNA940501	Zebrahub: Multimodal Zebrafish Developmental Atlas	PRJNA940501	Other	A single embryo single cell RNA seq developmental atlas of Zebrafish.			TDR18	TDR18 10somite EKW NA none 10x	strain:EKW\|isolate:single embryo\|breed:siblings per timepoint\|cultivar:not applicable\|ecotype:not applicable\|age:14 hpf\|sex:not determined\|tissue:Whole embryo\|replicate:rep1\|BioSampleModel:Model organism or animal								TDR18	TDR18 10somite EKW NA none 10x	TDR18 10somite EKW NA none 10x	single embryo dissociation		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425398		TDR18_10somite_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR18 10somite EKW NA none 10x S1 L001 I1 001.fastq.gz												SRX19554092		SRA1598656	Chan Zuckerberg Biohub\|Quantitative Cell Science	Chan Zuckerberg Biohub															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2023-03-02	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");;