metadata: run_metadata: 259 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "generic-scrnaseq-only" and tissue_curation

259 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	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.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.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
35567	35567	SRR32928199	SRX28203119	SRS24552825	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.F01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 6	100	100	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.enzymatic.P01.F01.fq.gz	fastq	800436.0	9529.0	expt2.broad.48.enzymatic.P01.F01.fq.gz	0:84	A:247920;C:168170;G:180799;T:203153;N:394	84		247920	168170	180799	203153	394	SRX28203119	SRS24552825	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35568	35568	SRR32928200	SRX28203118	SRS24552823	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.E01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 5	99	99	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.enzymatic.P01.E01.fq.gz	fastq	496356.0	5909.0	expt2.broad.48.enzymatic.P01.E01.fq.gz	0:84	A:156600;C:99183;G:113282;T:127036;N:255	84		156600	99183	113282	127036	255	SRX28203118	SRS24552823	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35569	35569	SRR32928201	SRX28203117	SRS24552824	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.D01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 4	98	98	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.enzymatic.P01.D01.fq.gz	fastq	2053800.0	24450.0	expt2.broad.48.enzymatic.P01.D01.fq.gz	0:84	A:668634;C:393806;G:431279;T:559022;N:1059	84		668634	393806	431279	559022	1059	SRX28203117	SRS24552824	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35570	35570	SRR32928202	SRX28203116	SRS24552821	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.C01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 3	97	97	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.enzymatic.P01.C01.fq.gz	fastq	2159052.0	25703.0	expt2.broad.48.enzymatic.P01.C01.fq.gz	0:84	A:837784;C:348085;G:463530;T:508544;N:1109	84		837784	348085	463530	508544	1109	SRX28203116	SRS24552821	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35571	35571	SRR32928203	SRX28203115	SRS24552822	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.B01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 2	96	96	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.enzymatic.P01.B01.fq.gz	fastq	3287508.0	39137.0	expt2.broad.48.enzymatic.P01.B01.fq.gz	0:84	A:1090202;C:644484;G:702124;T:848812;N:1886	84		1090202	644484	702124	848812	1886	SRX28203115	SRS24552822	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35572	35572	SRR32928204	SRX28203114	SRS24552819	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.enzymatic.P01.A01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 1	95	95	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.enzymatic.P01.A01.fq.gz	fastq	6623400.0	78850.0	expt2.broad.48.enzymatic.P01.A01.fq.gz	0:84	A:2915935;C:1012732;G:1256523;T:1434621;N:3589	84		2915935	1012732	1256523	1434621	3589	SRX28203114	SRS24552819	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35573	35573	SRR32928205	SRX28203113	SRS24552820	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.H02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:16\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 16	94	94	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.H02.fq.gz	fastq	18079152.0	215228.0	expt2.broad.48.bead.P18.H02.fq.gz	0:84	A:6013555;C:3409380;G:3853431;T:4793252;N:9534	84		6013555	3409380	3853431	4793252	9534	SRX28203113	SRS24552820	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35574	35574	SRR32928206	SRX28203112	SRS24552818	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.H01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:15\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 15	93	93	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.H01.fq.gz	fastq	13210764.0	157271.0	expt2.broad.48.bead.P18.H01.fq.gz	0:84	A:4207727;C:2577088;G:2821128;T:3597752;N:7069	84		4207727	2577088	2821128	3597752	7069	SRX28203112	SRS24552818	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35575	35575	SRR32928207	SRX28203111	SRS24552817	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.G02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:14\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 14	92	92	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.G02.fq.gz	fastq	14834736.0	176604.0	expt2.broad.48.bead.P18.G02.fq.gz	0:84	A:5041294;C:2753273;G:3108141;T:3924037;N:7991	84		5041294	2753273	3108141	3924037	7991	SRX28203111	SRS24552817	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35576	35576	SRR32928310	SRX28203110	SRS24552815	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.G12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 7	212	212	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.G12.fq.gz	fastq	25010412.0	297743.0	expt3.96.enzymatic.P18.G12.fq.gz	0:84	A:10964374;C:4064284;G:5105517;T:4873835;N:2402	84		10964374	4064284	5105517	4873835	2402	SRX28203110	SRS24552815	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35577	35577	SRR32928208	SRX28203109	SRS24552816	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.F12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 6	211	211	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.F12.fq.gz	fastq	34833876.0	414689.0	expt3.96.enzymatic.P18.F12.fq.gz	0:84	A:15190499;C:5741220;G:7109697;T:6789172;N:3288	84		15190499	5741220	7109697	6789172	3288	SRX28203109	SRS24552816	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35578	35578	SRR32928209	SRX28203108	SRS24552814	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.H3.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:22\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 22	22	22	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.H3.fq.gz	fastq	1098724956.0	13080059.0	expt1.12.bead.P1.H3.fq.gz	0:84	A:504518768;C:161484922;G:183535740;T:248983693;N:201833	84		504518768	161484922	183535740	248983693	201833	SRX28203108	SRS24552814	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35579	35579	SRR32928210	SRX28203107	SRS24552812	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.E12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 5	210	210	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.E12.fq.gz	fastq	27839784.0	331426.0	expt3.96.enzymatic.P18.E12.fq.gz	0:84	A:11930285;C:4560929;G:5811743;T:5534159;N:2668	84		11930285	4560929	5811743	5534159	2668	SRX28203107	SRS24552812	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35580	35580	SRR32928211	SRX28203106	SRS24552811	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.D12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 4	209	209	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.D12.fq.gz	fastq	27695556.0	329709.0	expt3.96.enzymatic.P18.D12.fq.gz	0:84	A:12091110;C:4491745;G:5609269;T:5500850;N:2582	84		12091110	4491745	5609269	5500850	2582	SRX28203106	SRS24552811	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35581	35581	SRR32928212	SRX28203105	SRS24552813	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.C12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 3	208	208	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.C12.fq.gz	fastq	24844932.0	295773.0	expt3.96.enzymatic.P18.C12.fq.gz	0:84	A:10700258;C:4111418;G:5035794;T:4994990;N:2472	84		10700258	4111418	5035794	4994990	2472	SRX28203105	SRS24552813	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35582	35582	SRR32928213	SRX28203104	SRS24552810	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.B12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 2	207	207	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.B12.fq.gz	fastq	10780812.0	128343.0	expt3.96.enzymatic.P18.B12.fq.gz	0:84	A:4635118;C:1860640;G:2120826;T:2163173;N:1055	84		4635118	1860640	2120826	2163173	1055	SRX28203104	SRS24552810	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.33865		0.22704		0.93659		0.55528		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35583	35583	SRR32928214	SRX28203103	SRS24552809	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt3.96.enzymatic.P18.A12.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 1	206	206	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.enzymatic.P18.A12.fq.gz	fastq	10534272.0	125408.0	expt3.96.enzymatic.P18.A12.fq.gz	0:84	A:4632079;C:1746502;G:2069269;T:2085448;N:974	84		4632079	1746502	2069269	2085448	974	SRX28203103	SRS24552809	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.33522		0.19264		0.93624		0.50295		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35584	35584	SRR32928215	SRX28203102	SRS24552808	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.H11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 8	205	205	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.H11.fq.gz	fastq	235038972.0	2798083.0	expt3.96.bead.P18.H11.fq.gz	0:84	A:85855798;C:40354173;G:45974107;T:62832438;N:22456	84		85855798	40354173	45974107	62832438	22456	SRX28203102	SRS24552808	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.61865		0.46937		0.80791		0.46334		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35585	35585	SRR32928216	SRX28203101	SRS24552807	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.G11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 7	204	204	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.G11.fq.gz	fastq	280436688.0	3338532.0	expt3.96.bead.P18.G11.fq.gz	0:84	A:105066150;C:48021700;G:54614521;T:72707589;N:26728	84		105066150	48021700	54614521	72707589	26728	SRX28203101	SRS24552807	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.59159		0.43599		0.80842		0.46679		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35586	35586	SRR32928217	SRX28203100	SRS24552806	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.F11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 6	203	203	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.F11.fq.gz	fastq	286313832.0	3408498.0	expt3.96.bead.P18.F11.fq.gz	0:84	A:106784155;C:49395267;G:55919780;T:74187078;N:27552	84		106784155	49395267	55919780	74187078	27552	SRX28203100	SRS24552806	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.60245		0.44424		0.81124		0.48908		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35587	35587	SRR32928218	SRX28203099	SRS24552804	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.E11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 5	202	202	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.E11.fq.gz	fastq	307881252.0	3665253.0	expt3.96.bead.P18.E11.fq.gz	0:84	A:115701302;C:52449337;G:59620790;T:80080256;N:29567	84		115701302	52449337	59620790	80080256	29567	SRX28203099	SRS24552804	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.5787		0.44122		0.81854		0.50262		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35588	35588	SRR32928219	SRX28203098	SRS24552803	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.D11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 4	201	201	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.D11.fq.gz	fastq	300632640.0	3578960.0	expt3.96.bead.P18.D11.fq.gz	0:84	A:113779580;C:51205126;G:58283346;T:77335567;N:29021	84		113779580	51205126	58283346	77335567	29021	SRX28203098	SRS24552803	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.57846		0.43882		0.81925		0.50496		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35589	35589	SRR32928220	SRX28203097	SRS24552805	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.G5.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:21\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 21	21	21	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.G5.fq.gz	fastq	561441468.0	6683827.0	expt1.12.bead.P1.G5.fq.gz	0:84	A:234940814;C:88191402;G:96728695;T:141478801;N:101756	84		234940814	88191402	96728695	141478801	101756	SRX28203097	SRS24552805	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.50019		0.4034		0.85959		0.49922		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35590	35590	SRR32928221	SRX28203096	SRS24552802	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.A5.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 3	3	3	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.A5.fq.gz	fastq	490718256.0	5841884.0	expt1.12.bead.P1.A5.fq.gz	0:84	A:207644706;C:75241234;G:85463387;T:122279492;N:89437	84		207644706	75241234	85463387	122279492	89437	SRX28203096	SRS24552802	SRA2104467	University of Washington\|Genome Sciences	University of Washington	1	0.50293		0.39872		0.85916		0.50964		84		B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35591	35591	SRR32928222	SRX28203095	SRS24552801	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.C11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 3	200	200	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.C11.fq.gz	fastq	269049312.0	3202968.0	expt3.96.bead.P18.C11.fq.gz	0:84	A:100635643;C:45939296;G:52190404;T:70258145;N:25824	84		100635643	45939296	52190404	70258145	25824	SRX28203095	SRS24552801	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35592	35592	SRR32928223	SRX28203094	SRS24552799	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.B11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 2	199	199	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.B11.fq.gz	fastq	123292428.0	1467767.0	expt3.96.bead.P18.B11.fq.gz	0:84	A:45529584;C:21218529;G:24007853;T:32524700;N:11762	84		45529584	21218529	24007853	32524700	11762	SRX28203094	SRS24552799	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35593	35593	SRR32928224	SRX28203093	SRS24552800	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.		expt3.96.bead.P18.A11.fq.gz	seq depth:NA\|Experiment id:3\|dissociation method:bead\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:96 hpf\|dev stage:96 hpf\|collection date:2024 03 19\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 1	198	198	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt3.96.bead.P18.A11.fq.gz	fastq	277357248.0	3301872.0	expt3.96.bead.P18.A11.fq.gz	0:84	A:105979207;C:47015802;G:54386470;T:69949155;N:26614	84		105979207	47015802	54386470	69949155	26614	SRX28203093	SRS24552800	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35594	35594	SRR32928225	SRX28203092	SRS24552798	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.H03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 8	197	197	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.H03.fq.gz	fastq	3437364.0	40921.0	expt2.deep.72.enzymatic.P01.H03.fq.gz	0:84	A:1374051;C:578097;G:717673;T:766942;N:601	84		1374051	578097	717673	766942	601	SRX28203092	SRS24552798	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35595	35595	SRR32928226	SRX28203091	SRS24552797	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.G03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 7	196	196	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.G03.fq.gz	fastq	8559096.0	101894.0	expt2.deep.72.enzymatic.P01.G03.fq.gz	0:84	A:3252394;C:1515721;G:1860485;T:1929016;N:1480	84		3252394	1515721	1860485	1929016	1480	SRX28203091	SRS24552797	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35596	35596	SRR32928227	SRX28203090	SRS24552795	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.F03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 6	195	195	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.F03.fq.gz	fastq	86570988.0	1030607.0	expt2.deep.72.enzymatic.P01.F03.fq.gz	0:84	A:39076701;C:15258279;G:16117195;T:16103299;N:15514	84		39076701	15258279	16117195	16103299	15514	SRX28203090	SRS24552795	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35597	35597	SRR32928228	SRX28203089	SRS24552796	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.E03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 5	194	194	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.E03.fq.gz	fastq	21496020.0	255905.0	expt2.deep.72.enzymatic.P01.E03.fq.gz	0:84	A:7897723;C:3941227;G:4608642;T:5044562;N:3866	84		7897723	3941227	4608642	5044562	3866	SRX28203089	SRS24552796	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35598	35598	SRR32928229	SRX28203088	SRS24552794	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.D03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 4	193	193	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.D03.fq.gz	fastq	38955504.0	463756.0	expt2.deep.72.enzymatic.P01.D03.fq.gz	0:84	A:18141798;C:6097971;G:8057753;T:6650850;N:7132	84		18141798	6097971	8057753	6650850	7132	SRX28203088	SRS24552794	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35599	35599	SRR32928230	SRX28203087	SRS24552793	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.C03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 3	192	192	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.C03.fq.gz	fastq	51870336.0	617504.0	expt2.deep.72.enzymatic.P01.C03.fq.gz	0:84	A:17090212;C:9836274;G:12030231;T:12904330;N:9289	84		17090212	9836274	12030231	12904330	9289	SRX28203087	SRS24552793	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35600	35600	SRR32928231	SRX28203086	SRS24552791	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.B03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 2	191	191	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.B03.fq.gz	fastq	14069832.0	167498.0	expt2.deep.72.enzymatic.P01.B03.fq.gz	0:84	A:5389848;C:2403134;G:3075076;T:3199255;N:2519	84		5389848	2403134	3075076	3199255	2519	SRX28203086	SRS24552791	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35601	35601	SRR32928232	SRX28203085	SRS24552792	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.G4.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:20\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 20	20	20	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.G4.fq.gz	fastq	515444412.0	6136243.0	expt1.12.bead.P1.G4.fq.gz	0:84	A:215225166;C:80082472;G:88915670;T:131127655;N:93449	84		215225166	80082472	88915670	131127655	93449	SRX28203085	SRS24552792	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35602	35602	SRR32928233	SRX28203084	SRS24552790	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.enzymatic.P01.A03.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 1	190	190	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.enzymatic.P01.A03.fq.gz	fastq	218177316.0	2597349.0	expt2.deep.72.enzymatic.P01.A03.fq.gz	0:84	A:102730118;C:32493129;G:39547427;T:43367265;N:39377	84		102730118	32493129	39547427	43367265	39377	SRX28203084	SRS24552790	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35603	35603	SRR32928234	SRX28203083	SRS24552789	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.G01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:13\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 13	91	91	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.G01.fq.gz	fastq	14202468.0	169077.0	expt2.broad.48.bead.P18.G01.fq.gz	0:84	A:4692822;C:2685182;G:2975257;T:3841545;N:7662	84		4692822	2685182	2975257	3841545	7662	SRX28203083	SRS24552789	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35604	35604	SRR32928235	SRX28203082	SRS24552787	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.D3.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:10\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 10	10	10	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.D3.fq.gz	fastq	629856780.0	7498295.0	expt1.12.bead.P1.D3.fq.gz	0:84	A:273859568;C:96165073;G:108875157;T:150842309;N:114673	84		273859568	96165073	108875157	150842309	114673	SRX28203082	SRS24552787	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35605	35605	SRR32928236	SRX28203081	SRS24552788	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.F02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:12\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 12	90	90	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.F02.fq.gz	fastq	16051728.0	191092.0	expt2.broad.48.bead.P18.F02.fq.gz	0:84	A:5221193;C:3079215;G:3420876;T:4321889;N:8555	84		5221193	3079215	3420876	4321889	8555	SRX28203081	SRS24552788	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35606	35606	SRR32928237	SRX28203080	SRS24552786	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.F01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:11\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 11	89	89	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.F01.fq.gz	fastq	19022388.0	226457.0	expt2.broad.48.bead.P18.F01.fq.gz	0:84	A:6375349;C:3646304;G:4032366;T:4958089;N:10280	84		6375349	3646304	4032366	4958089	10280	SRX28203080	SRS24552786	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35607	35607	SRR32928238	SRX28203079	SRS24552785	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.E02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:10\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 10	88	88	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.E02.fq.gz	fastq	17436720.0	207580.0	expt2.broad.48.bead.P18.E02.fq.gz	0:84	A:5912075;C:3260546;G:3682832;T:4572094;N:9173	84		5912075	3260546	3682832	4572094	9173	SRX28203079	SRS24552785	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35608	35608	SRR32928239	SRX28203078	SRS24552783	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.E01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:9\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 9	87	87	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.E01.fq.gz	fastq	12759768.0	151902.0	expt2.broad.48.bead.P18.E01.fq.gz	0:84	A:4143321;C:2424389;G:2695567;T:3489773;N:6718	84		4143321	2424389	2695567	3489773	6718	SRX28203078	SRS24552783	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35609	35609	SRR32928240	SRX28203077	SRS24552784	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.D02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 8	86	86	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.D02.fq.gz	fastq	17226132.0	205073.0	expt2.broad.48.bead.P18.D02.fq.gz	0:84	A:5722683;C:3229414;G:3698323;T:4566519;N:9193	84		5722683	3229414	3698323	4566519	9193	SRX28203077	SRS24552784	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35610	35610	SRR32928241	SRX28203076	SRS24552782	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.D01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 7	85	85	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.D01.fq.gz	fastq	14390124.0	171311.0	expt2.broad.48.bead.P18.D01.fq.gz	0:84	A:4584304;C:2823369;G:3092301;T:3882609;N:7541	84		4584304	2823369	3092301	3882609	7541	SRX28203076	SRS24552782	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35611	35611	SRR32928242	SRX28203075	SRS24552781	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.C02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 6	84	84	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.C02.fq.gz	fastq	18592560.0	221340.0	expt2.broad.48.bead.P18.C02.fq.gz	0:84	A:6370777;C:3468105;G:3988886;T:4754942;N:9850	84		6370777	3468105	3988886	4754942	9850	SRX28203075	SRS24552781	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35612	35612	SRR32928243	SRX28203074	SRS24552780	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.C01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 5	83	83	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.C01.fq.gz	fastq	12557076.0	149489.0	expt2.broad.48.bead.P18.C01.fq.gz	0:84	A:3977371;C:2443832;G:2711905;T:3417301;N:6667	84		3977371	2443832	2711905	3417301	6667	SRX28203074	SRS24552780	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35613	35613	SRR32928244	SRX28203073	SRS24552779	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.B02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 4	82	82	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.B02.fq.gz	fastq	14289828.0	170117.0	expt2.broad.48.bead.P18.B02.fq.gz	0:84	A:4795697;C:2698305;G:3083373;T:3704963;N:7490	84		4795697	2698305	3083373	3704963	7490	SRX28203073	SRS24552779	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35614	35614	SRR32928245	SRX28203072	SRS24552778	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.B01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 3	81	81	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.B01.fq.gz	fastq	6255144.0	74466.0	expt2.broad.48.bead.P18.B01.fq.gz	0:84	A:1953811;C:1213806;G:1335743;T:1748533;N:3251	84		1953811	1213806	1335743	1748533	3251	SRX28203072	SRS24552778	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35615	35615	SRR32928246	SRX28203071	SRS24552777	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.C5.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:9\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 9	9	9	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.C5.fq.gz	fastq	461470968.0	5493702.0	expt1.12.bead.P1.C5.fq.gz	0:84	A:188895160;C:72428601;G:79983141;T:120080226;N:83840	84		188895160	72428601	79983141	120080226	83840	SRX28203071	SRS24552777	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35616	35616	SRR32928247	SRX28203070	SRS24552776	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.A02.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 2	80	80	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.A02.fq.gz	fastq	16441656.0	195734.0	expt2.broad.48.bead.P18.A02.fq.gz	0:84	A:5495147;C:3127531;G:3493145;T:4317176;N:8657	84		5495147	3127531	3493145	4317176	8657	SRX28203070	SRS24552776	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35617	35617	SRR32928248	SRX28203069	SRS24552775	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.48.bead.P18.A01.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:bead\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 1	79	79	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.48.bead.P18.A01.fq.gz	fastq	14319564.0	170471.0	expt2.broad.48.bead.P18.A01.fq.gz	0:84	A:4614154;C:2749141;G:3043759;T:3904988;N:7522	84		4614154	2749141	3043759	3904988	7522	SRX28203069	SRS24552775	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35618	35618	SRR32928249	SRX28203068	SRS24552774	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.H05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 8	78	78	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.H05.fq.gz	fastq	9110220.0	108455.0	expt2.broad.24.enzymatic.P01.H05.fq.gz	0:84	A:3384792;C:1565195;G:1973031;T:2182427;N:4775	84		3384792	1565195	1973031	2182427	4775	SRX28203068	SRS24552774	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35619	35619	SRR32928250	SRX28203067	SRS24552773	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.G05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 7	77	77	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.G05.fq.gz	fastq	4093068.0	48727.0	expt2.broad.24.enzymatic.P01.G05.fq.gz	0:84	A:1283703;C:801390;G:874961;T:1130908;N:2106	84		1283703	801390	874961	1130908	2106	SRX28203067	SRS24552773	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35620	35620	SRR32928251	SRX28203066	SRS24552772	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.F05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 6	76	76	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.F05.fq.gz	fastq	15414840.0	183510.0	expt2.broad.24.enzymatic.P01.F05.fq.gz	0:84	A:6868692;C:2274988;G:2950304;T:3312556;N:8300	84		6868692	2274988	2950304	3312556	8300	SRX28203066	SRS24552772	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35621	35621	SRR32928252	SRX28203065	SRS24552771	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.E05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 5	75	75	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.E05.fq.gz	fastq	7552440.0	89910.0	expt2.broad.24.enzymatic.P01.E05.fq.gz	0:84	A:2833004;C:1314546;G:1543833;T:1856906;N:4151	84		2833004	1314546	1543833	1856906	4151	SRX28203065	SRS24552771	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35622	35622	SRR32928253	SRX28203064	SRS24552770	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.D05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 4	74	74	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.D05.fq.gz	fastq	18449592.0	219638.0	expt2.broad.24.enzymatic.P01.D05.fq.gz	0:84	A:8110605;C:2781954;G:3613141;T:3933803;N:10089	84		8110605	2781954	3613141	3933803	10089	SRX28203064	SRS24552770	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35623	35623	SRR32928254	SRX28203063	SRS24552769	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.C05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 3	73	73	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.C05.fq.gz	fastq	5944344.0	70766.0	expt2.broad.24.enzymatic.P01.C05.fq.gz	0:84	A:2038886;C:1067891;G:1274553;T:1559956;N:3058	84		2038886	1067891	1274553	1559956	3058	SRX28203063	SRS24552769	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35624	35624	SRR32928255	SRX28203062	SRS24552768	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.B05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 2	72	72	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.B05.fq.gz	fastq	8608320.0	102480.0	expt2.broad.24.enzymatic.P01.B05.fq.gz	0:84	A:3054837;C:1594241;G:1754868;T:2199803;N:4571	84		3054837	1594241	1754868	2199803	4571	SRX28203062	SRS24552768	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35625	35625	SRR32928256	SRX28203061	SRS24552767	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.		expt2.broad.24.enzymatic.P01.A05.fq.gz	seq depth:broad many cells\|Experiment id:2\|dissociation method:enzymatic\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf\|dev stage:24 hpf\|collection date:2024 01 30\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 1	71	71	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.broad.24.enzymatic.P01.A05.fq.gz	fastq	3979164.0	47371.0	expt2.broad.24.enzymatic.P01.A05.fq.gz	0:84	A:1268971;C:764759;G:844472;T:1098812;N:2150	84		1268971	764759	844472	1098812	2150	SRX28203061	SRS24552767	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
35626	35626	SRR32928257	SRX28203060	SRS24552766	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.C4.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 8	8	8	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.C4.fq.gz	fastq	451683456.0	5377184.0	expt1.12.bead.P1.C4.fq.gz	0:84	A:188077465;C:71524093;G:79688471;T:112311489;N:81938	84		188077465	71524093	79688471	112311489	81938	SRX28203060	SRS24552766	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35627	35627	SRR32928258	SRX28203059	SRS24552765	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.H05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:16\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 16	189	189	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.H05.fq.gz	fastq	100072896.0	1191344.0	expt2.deep.72.bead.P18.H05.fq.gz	0:84	A:37670921;C:17233514;G:20449798;T:24701130;N:17533	84		37670921	17233514	20449798	24701130	17533	SRX28203059	SRS24552765	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35628	35628	SRR32928259	SRX28203058	SRS24552764	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.H04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:15\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 15	188	188	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.H04.fq.gz	fastq	127374408.0	1516362.0	expt2.deep.72.bead.P18.H04.fq.gz	0:84	A:49385711;C:21752310;G:26316853;T:29896958;N:22576	84		49385711	21752310	26316853	29896958	22576	SRX28203058	SRS24552764	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35629	35629	SRR32928260	SRX28203057	SRS24552763	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.G05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:14\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 14	187	187	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.G05.fq.gz	fastq	118781376.0	1414064.0	expt2.deep.72.bead.P18.G05.fq.gz	0:84	A:46475832;C:19993091;G:24438008;T:27853488;N:20957	84		46475832	19993091	24438008	27853488	20957	SRX28203057	SRS24552763	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35630	35630	SRR32928261	SRX28203056	SRS24552760	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.G04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:13\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 13	186	186	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.G04.fq.gz	fastq	129283728.0	1539092.0	expt2.deep.72.bead.P18.G04.fq.gz	0:84	A:51256657;C:21906239;G:26113882;T:29984084;N:22866	84		51256657	21906239	26113882	29984084	22866	SRX28203056	SRS24552760	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35631	35631	SRR32928262	SRX28203055	SRS24552761	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.F05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:12\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 12	185	185	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.F05.fq.gz	fastq	129148404.0	1537481.0	expt2.deep.72.bead.P18.F05.fq.gz	0:84	A:49582957;C:22353347;G:27049287;T:30139940;N:22873	84		49582957	22353347	27049287	30139940	22873	SRX28203055	SRS24552761	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35632	35632	SRR32928263	SRX28203054	SRS24552762	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.F04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:11\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 11	184	184	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.F04.fq.gz	fastq	150033996.0	1786119.0	expt2.deep.72.bead.P18.F04.fq.gz	0:84	A:58692014;C:25506404;G:31365137;T:34443610;N:26831	84		58692014	25506404	31365137	34443610	26831	SRX28203054	SRS24552762	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35633	35633	SRR32928264	SRX28203053	SRS24552759	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.E05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:10\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 10	183	183	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.E05.fq.gz	fastq	126694176.0	1508264.0	expt2.deep.72.bead.P18.E05.fq.gz	0:84	A:51627607;C:20422286;G:26199504;T:28422124;N:22655	84		51627607	20422286	26199504	28422124	22655	SRX28203053	SRS24552759	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35634	35634	SRR32928265	SRX28203052	SRS24552758	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.E04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:9\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 9	182	182	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.E04.fq.gz	fastq	116357388.0	1385207.0	expt2.deep.72.bead.P18.E04.fq.gz	0:84	A:44265643;C:20201353;G:23492981;T:28376788;N:20623	84		44265643	20201353	23492981	28376788	20623	SRX28203052	SRS24552758	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35635	35635	SRR32928266	SRX28203051	SRS24552756	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.D05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 8	181	181	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.D05.fq.gz	fastq	108267516.0	1288899.0	expt2.deep.72.bead.P18.D05.fq.gz	0:84	A:41225423;C:18528370;G:22265524;T:26229153;N:19046	84		41225423	18528370	22265524	26229153	19046	SRX28203051	SRS24552756	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35636	35636	SRR32928267	SRX28203050	SRS24552757	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.G3.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:19\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 19	19	19	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.G3.fq.gz	fastq	615903456.0	7332184.0	expt1.12.bead.P1.G3.fq.gz	0:84	A:262286368;C:93846834;G:105834930;T:153823652;N:111672	84		262286368	93846834	105834930	153823652	111672	SRX28203050	SRS24552757	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35637	35637	SRR32928268	SRX28203049	SRS24552755	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.D04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 7	180	180	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.D04.fq.gz	fastq	179121432.0	2132398.0	expt2.deep.72.bead.P18.D04.fq.gz	0:84	A:72040384;C:30579403;G:36178369;T:40291119;N:32157	84		72040384	30579403	36178369	40291119	32157	SRX28203049	SRS24552755	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35638	35638	SRR32928269	SRX28203048	SRS24552754	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.C05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 6	179	179	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.C05.fq.gz	fastq	127961736.0	1523354.0	expt2.deep.72.bead.P18.C05.fq.gz	0:84	A:51654447;C:20918642;G:25857491;T:29508510;N:22646	84		51654447	20918642	25857491	29508510	22646	SRX28203048	SRS24552754	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35639	35639	SRR32928270	SRX28203047	SRS24552752	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.C04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 5	178	178	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.C04.fq.gz	fastq	146400408.0	1742862.0	expt2.deep.72.bead.P18.C04.fq.gz	0:84	A:55629641;C:25211316;G:31130733;T:34402847;N:25871	84		55629641	25211316	31130733	34402847	25871	SRX28203047	SRS24552752	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35640	35640	SRR32928271	SRX28203046	SRS24552753	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.B05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 4	177	177	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.B05.fq.gz	fastq	117954144.0	1404216.0	expt2.deep.72.bead.P18.B05.fq.gz	0:84	A:44956751;C:20285211;G:23912754;T:28778491;N:20937	84		44956751	20285211	23912754	28778491	20937	SRX28203046	SRS24552753	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35641	35641	SRR32928272	SRX28203045	SRS24552751	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.B04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 3	176	176	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.B04.fq.gz	fastq	130428480.0	1552720.0	expt2.deep.72.bead.P18.B04.fq.gz	0:84	A:50376868;C:21973684;G:26967945;T:31086704;N:23279	84		50376868	21973684	26967945	31086704	23279	SRX28203045	SRS24552751	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35642	35642	SRR32928273	SRX28203044	SRS24552750	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.A05.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:2\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 2	175	175	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.A05.fq.gz	fastq	112201572.0	1335733.0	expt2.deep.72.bead.P18.A05.fq.gz	0:84	A:43113841;C:19396291;G:22746828;T:26924715;N:19897	84		43113841	19396291	22746828	26924715	19897	SRX28203044	SRS24552750	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35643	35643	SRR32928274	SRX28203043	SRS24552749	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.72.bead.P18.A04.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:bead\|replicate:1\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:72 hpf\|dev stage:72 hpf\|collection date:2024 02 01\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 1	174	174	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.72.bead.P18.A04.fq.gz	fastq	104432076.0	1243239.0	expt2.deep.72.bead.P18.A04.fq.gz	0:84	A:38988959;C:18551135;G:21469977;T:25403610;N:18395	84		38988959	18551135	21469977	25403610	18395	SRX28203043	SRS24552749	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Larval	Larval	Whole Organism	All anatomical structures
35644	35644	SRR32928275	SRX28203042	SRS24552748	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.48.enzymatic.P01.H01.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:8\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 48hpf enzymatic dissociation replicate 8	173	173	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.48.enzymatic.P01.H01.fq.gz	fastq	10952424.0	130386.0	expt2.deep.48.enzymatic.P01.H01.fq.gz	0:84	A:3876382;C:2009479;G:2298766;T:2765953;N:1844	84		3876382	2009479	2298766	2765953	1844	SRX28203042	SRS24552748	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35645	35645	SRR32928276	SRX28203041	SRS24552747	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.48.enzymatic.P01.G01.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:7\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 48hpf enzymatic dissociation replicate 7	172	172	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.48.enzymatic.P01.G01.fq.gz	fastq	14085792.0	167688.0	expt2.deep.48.enzymatic.P01.G01.fq.gz	0:84	A:5224461;C:2624861;G:2935295;T:3298694;N:2481	84		5224461	2624861	2935295	3298694	2481	SRX28203041	SRS24552747	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35646	35646	SRR32928277	SRX28203040	SRS24552746	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.48.enzymatic.P01.F01.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:6\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 48hpf enzymatic dissociation replicate 6	171	171	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.48.enzymatic.P01.F01.fq.gz	fastq	9595404.0	114231.0	expt2.deep.48.enzymatic.P01.F01.fq.gz	0:84	A:3301852;C:1874682;G:2048715;T:2368498;N:1657	84		3301852	1874682	2048715	2368498	1657	SRX28203040	SRS24552746	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35647	35647	SRR32928278	SRX28203039	SRS24552745	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.F5.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:18\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 18	18	18	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.F5.fq.gz	fastq	470902236.0	5605979.0	expt1.12.bead.P1.F5.fq.gz	0:84	A:195943515;C:74075531;G:81085740;T:119712297;N:85153	84		195943515	74075531	81085740	119712297	85153	SRX28203039	SRS24552745	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35648	35648	SRR32928279	SRX28203038	SRS24552744	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.48.enzymatic.P01.E01.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 48hpf enzymatic dissociation replicate 5	170	170	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.48.enzymatic.P01.E01.fq.gz	fastq	6317472.0	75208.0	expt2.deep.48.enzymatic.P01.E01.fq.gz	0:84	A:2175918;C:1173989;G:1412172;T:1554313;N:1080	84		2175918	1173989	1412172	1554313	1080	SRX28203038	SRS24552744	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35649	35649	SRR32928280	SRX28203037	SRS24552743	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.48.enzymatic.P01.D01.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:4\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 48hpf enzymatic dissociation replicate 4	169	169	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.48.enzymatic.P01.D01.fq.gz	fastq	26805408.0	319112.0	expt2.deep.48.enzymatic.P01.D01.fq.gz	0:84	A:9489671;C:4847582;G:5421907;T:7041421;N:4827	84		9489671	4847582	5421907	7041421	4827	SRX28203037	SRS24552743	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35650	35650	SRR32928281	SRX28203036	SRS24552742	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.		expt2.deep.48.enzymatic.P01.C01.fq.gz	seq depth:deep many umis\|Experiment id:2\|dissociation method:enzymatic\|replicate:3\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf\|dev stage:48 hpf\|collection date:2024 01 31\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 48hpf enzymatic dissociation replicate 3	168	168	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt2.deep.48.enzymatic.P01.C01.fq.gz	fastq	37386300.0	445075.0	expt2.deep.48.enzymatic.P01.C01.fq.gz	0:84	A:15837274;C:5306422;G:7863430;T:8372443;N:6731	84		15837274	5306422	7863430	8372443	6731	SRX28203036	SRS24552742	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Hatching	Embryo	Whole Organism	All anatomical structures
35651	35651	SRR32928360	SRX28203035	SRS24552741	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.F9.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:23\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 23	47	47	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.F9.fq.gz	fastq	65463048.0	779322.0	expt1.12.enzymatic.P18.F9.fq.gz	0:84	A:26680121;C:10235479;G:11460930;T:17074778;N:11740	84		26680121	10235479	11460930	17074778	11740	SRX28203035	SRS24552741	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35652	35652	SRR32928282	SRX28203034	SRS24552740	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.F12.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:22\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 22	46	46	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.F12.fq.gz	fastq	78852564.0	938721.0	expt1.12.enzymatic.P18.F12.fq.gz	0:84	A:31835768;C:12617722;G:13918857;T:20465816;N:14401	84		31835768	12617722	13918857	20465816	14401	SRX28203034	SRS24552740	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35653	35653	SRR32928283	SRX28203033	SRS24552739	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.F11.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:21\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 21	45	45	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.F11.fq.gz	fastq	48518148.0	577597.0	expt1.12.enzymatic.P18.F11.fq.gz	0:84	A:19703045;C:7650268;G:8411266;T:12744788;N:8781	84		19703045	7650268	8411266	12744788	8781	SRX28203033	SRS24552739	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35654	35654	SRR32928284	SRX28203032	SRS24552738	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.F10.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:20\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 20	44	44	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.F10.fq.gz	fastq	69879012.0	831893.0	expt1.12.enzymatic.P18.F10.fq.gz	0:84	A:28102461;C:11066956;G:12285446;T:18411491;N:12658	84		28102461	11066956	12285446	18411491	12658	SRX28203032	SRS24552738	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35655	35655	SRR32928285	SRX28203031	SRS24552737	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.E9.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:19\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 19	43	43	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.E9.fq.gz	fastq	73466652.0	874603.0	expt1.12.enzymatic.P18.E9.fq.gz	0:84	A:30049012;C:11512079;G:12932629;T:18959717;N:13215	84		30049012	11512079	12932629	18959717	13215	SRX28203031	SRS24552737	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35656	35656	SRR32928286	SRX28203030	SRS24552736	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.E12.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:18\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 18	42	42	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.E12.fq.gz	fastq	46559856.0	554284.0	expt1.12.enzymatic.P18.E12.fq.gz	0:84	A:18707105;C:7369117;G:8285427;T:12189718;N:8489	84		18707105	7369117	8285427	12189718	8489	SRX28203030	SRS24552736	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35657	35657	SRR32928287	SRX28203029	SRS24552735	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.E11.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:17\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 17	41	41	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.E11.fq.gz	fastq	50957256.0	606634.0	expt1.12.enzymatic.P18.E11.fq.gz	0:84	A:20649122;C:8019708;G:8855871;T:13423308;N:9247	84		20649122	8019708	8855871	13423308	9247	SRX28203029	SRS24552735	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35658	35658	SRR32928288	SRX28203028	SRS24552733	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.		expt1.12.bead.P1.B4.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:bead\|replicate:5\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 08\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 5	5	5	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.bead.P1.B4.fq.gz	fastq	615855072.0	7331608.0	expt1.12.bead.P1.B4.fq.gz	0:84	A:259160966;C:97496208;G:105354232;T:153731811;N:111855	84		259160966	97496208	105354232	153731811	111855	SRX28203028	SRS24552733	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35659	35659	SRR32928289	SRX28203027	SRS24552734	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.E10.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:16\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 16	40	40	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.E10.fq.gz	fastq	69996948.0	833297.0	expt1.12.enzymatic.P18.E10.fq.gz	0:84	A:28524785;C:10983741;G:12267049;T:18208598;N:12775	84		28524785	10983741	12267049	18208598	12775	SRX28203027	SRS24552734	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35660	35660	SRR32928290	SRX28203026	SRS24552732	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.D9.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:15\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 15	39	39	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.D9.fq.gz	fastq	80656128.0	960192.0	expt1.12.enzymatic.P18.D9.fq.gz	0:84	A:33056742;C:12587584;G:14103652;T:20893622;N:14528	84		33056742	12587584	14103652	20893622	14528	SRX28203026	SRS24552732	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35661	35661	SRR32928291	SRX28203025	SRS24552731	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.D12.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:14\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 14	38	38	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.D12.fq.gz	fastq	51854880.0	617320.0	expt1.12.enzymatic.P18.D12.fq.gz	0:84	A:21118580;C:8107436;G:9141499;T:13477955;N:9410	84		21118580	8107436	9141499	13477955	9410	SRX28203025	SRS24552731	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35662	35662	SRR32928292	SRX28203024	SRS24552730	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.D11.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:13\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 13	37	37	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.D11.fq.gz	fastq	69585180.0	828395.0	expt1.12.enzymatic.P18.D11.fq.gz	0:84	A:27942625;C:11138327;G:12428227;T:18063636;N:12365	84		27942625	11138327	12428227	18063636	12365	SRX28203024	SRS24552730	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35663	35663	SRR32928293	SRX28203023	SRS24552728	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.D10.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:12\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 12	36	36	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.D10.fq.gz	fastq	83209140.0	990585.0	expt1.12.enzymatic.P18.D10.fq.gz	0:84	A:33904149;C:13026403;G:14694719;T:21568684;N:15185	84		33904149	13026403	14694719	21568684	15185	SRX28203023	SRS24552728	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	Segmentation	Embryo	Whole Organism	All anatomical structures
35664	35664	SRR32928294	SRX28203022	SRS24552729	SRP575522	PRJNA1244443	An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing	PRJNA1244443	Other	Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.		Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using enzymatic digestion.		expt1.12.enzymatic.P18.C9.fq.gz	seq depth:NA\|Experiment id:1\|dissociation method:enzymatic\|replicate:11\|strain:AB\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf\|dev stage:8 somite\|collection date:2024 03 05\|geo loc name:USA:Washington Seattle\|sex:not collected\|tissue:Whole Embryo\|sample type:Whole organism\|BioSampleModel:Model organism or animal							sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf enzymatic dissociation replicate 11	35	35	Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.		OTHER	TRANSCRIPTOMIC SINGLE CELL	other	SINGLE	ILLUMINA	NextSeq 2000	SRP575522	expt1.12.enzymatic.P18.C9.fq.gz	fastq	66058944.0	786416.0	expt1.12.enzymatic.P18.C9.fq.gz	0:84	A:26767185;C:10402625;G:11677135;T:17200217;N:11782	84		26767185	10402625	11677135	17200217	11782	SRX28203022	SRS24552729	SRA2104467	University of Washington\|Genome Sciences	University of Washington												B		usable mapping rate	illumina	nextseq_v2	unknown	other	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-03-31	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");;