metadata: run_metadata: 230 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "generic-scrnaseq-only"

230 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "generic-scrnaseq-only"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
19476	19476	ERR14208827	ERX13611047	ERS22979745	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	Scrambled 1 sample	SAMEA117628607	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 004\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 004\|scientific name:Danio rerio	Raw reads: Scrambled 1 sample	webin reads Scrambled 1 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: Scrambled 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F04.bam	bam	8497741.0	104283.0	webin reads Scrambled 1 sample	0:81.49	A:2628864;C:1112827;G:2146146;T:2609768;N:136	81	2628864	1112827	2146146	2609768	136	ERX13611047	ERS22979745	ERA31123309	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19477	19477	ERR14208813	ERX13611033	ERS22979748	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	ythdf2KO 1 sample	SAMEA117628610	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 007\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 007\|scientific name:Danio rerio	Raw reads: ythdf2KO 1 sample	webin reads ythdf2KO 1 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D09.bam	bam	673213184.0	8122011.0	webin reads ythdf2KO 1 sample	0:82.89	A:180836688;C:107076381;G:193711319;T:191586188;N:2608	82	180836688	107076381	193711319	191586188	2608	ERX13611033	ERS22979748	ERA31123295	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19478	19478	ERR14208811	ERX13611031	ERS22979755	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	GFP 6 sample	SAMEA117628617	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 014\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 014\|scientific name:Danio rerio	Raw reads: GFP 6 sample	webin reads GFP 6 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 6 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	H01.bam	bam	337553787.0	3153658.0	webin reads GFP 6 sample	0:107.04	A:81816649;C:55524538;G:113686171;T:86525390;N:1039	107	81816649	55524538	113686171	86525390	1039	ERX13611031	ERS22979755	ERA31123293	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19479	19479	ERR14208821	ERX13611041	ERS22979752	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	ythdf2KO 5 sample	SAMEA117628614	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 011\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 011\|scientific name:Danio rerio	Raw reads: ythdf2KO 5 sample	webin reads ythdf2KO 5 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 5 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G10.bam	bam	226771232.0	2050630.0	webin reads ythdf2KO 5 sample	0:110.59	A:56944731;C:30766256;G:83820146;T:55239221;N:878	110	56944731	30766256	83820146	55239221	878	ERX13611041	ERS22979752	ERA31123303	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19480	19480	ERR14208818	ERX13611038	ERS22979750	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	ythdf2KO 3 sample	SAMEA117628612	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 009\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 009\|scientific name:Danio rerio	Raw reads: ythdf2KO 3 sample	webin reads ythdf2KO 3 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G08.bam	bam	351425328.0	3771763.0	webin reads ythdf2KO 3 sample	0:93.17	A:83933175;C:50138103;G:128300798;T:89051913;N:1339	93	83933175	50138103	128300798	89051913	1339	ERX13611038	ERS22979750	ERA31123300	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19481	19481	ERR14208826	ERX13611046	ERS22979758	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	YTHDF2 3 sample	SAMEA117628620	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 017\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 017\|scientific name:Danio rerio	Raw reads: YTHDF2 3 sample	webin reads YTHDF2 3 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: YTHDF2 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	E01.bam	bam	181017083.0	1670383.0	webin reads YTHDF2 3 sample	0:108.37	A:38910474;C:31607688;G:67095095;T:43403227;N:599	108	38910474	31607688	67095095	43403227	599	ERX13611046	ERS22979758	ERA31123308	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19482	19482	ERR14208815	ERX13611035	ERS22979749	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	ythdf2KO 2 sample	SAMEA117628611	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 008\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 008\|scientific name:Danio rerio	Raw reads: ythdf2KO 2 sample	webin reads ythdf2KO 2 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D10.bam	bam	282414832.0	2675188.0	webin reads ythdf2KO 2 sample	0:105.57	A:73651155;C:41694223;G:96485766;T:70582706;N:982	105	73651155	41694223	96485766	70582706	982	ERX13611035	ERS22979749	ERA31123297	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19483	19483	ERR14208804	ERX13611024	ERS22979742	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	GFP 1 sample	SAMEA117628604	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 001\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 001\|scientific name:Danio rerio	Raw reads: GFP 1 sample	webin reads GFP 1 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F01.bam	bam	8036009.0	97716.0	webin reads GFP 1 sample	0:82.24	A:2445867;C:1074319;G:2086526;T:2429153;N:144	82	2445867	1074319	2086526	2429153	144	ERX13611024	ERS22979742	ERA31123286	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19484	19484	ERR14208829	ERX13611049	ERS22979747	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	Scrambled 3 sample	SAMEA117628609	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 006\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 006\|scientific name:Danio rerio	Raw reads: Scrambled 3 sample	webin reads Scrambled 3 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: Scrambled 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F06.bam	bam	90051514.0	910768.0	webin reads Scrambled 3 sample	0:98.87	A:30132090;C:13700682;G:16323331;T:29894332;N:1079	98	30132090	13700682	16323331	29894332	1079	ERX13611049	ERS22979747	ERA31123311	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19485	19485	ERR14208809	ERX13611029	ERS22979753	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	GFP 4 sample	SAMEA117628615	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 012\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 012\|scientific name:Danio rerio	Raw reads: GFP 4 sample	webin reads GFP 4 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 4 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G11.bam	bam	72278736.0	751207.0	webin reads GFP 4 sample	0:96.22	A:17589630;C:11153310;G:25212154;T:18323416;N:226	96	17589630	11153310	25212154	18323416	226	ERX13611029	ERS22979753	ERA31123291	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19486	19486	ERR14208806	ERX13611026	ERS22979743	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	GFP 2 sample	SAMEA117628605	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 002\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 002\|scientific name:Danio rerio	Raw reads: GFP 2 sample	webin reads GFP 2 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F02.bam	bam	19196592.0	230075.0	webin reads GFP 2 sample	0:83.44	A:5957309;C:2709511;G:4434875;T:6094552;N:345	83	5957309	2709511	4434875	6094552	345	ERX13611026	ERS22979743	ERA31123288	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19487	19487	ERR14208810	ERX13611030	ERS22979754	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	GFP 5 sample	SAMEA117628616	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 013\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 013\|scientific name:Danio rerio	Raw reads: GFP 5 sample	webin reads GFP 5 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 5 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G12.bam	bam	431708790.0	5173015.0	webin reads GFP 5 sample	0:83.45	A:119077902;C:68329173;G:126879243;T:117420803;N:1669	83	119077902	68329173	126879243	117420803	1669	ERX13611030	ERS22979754	ERA31123292	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19488	19488	ERR14208828	ERX13611048	ERS22979746	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	Scrambled 2 sample	SAMEA117628608	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 005\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 005\|scientific name:Danio rerio	Raw reads: Scrambled 2 sample	webin reads Scrambled 2 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: Scrambled 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F05.bam	bam	32695808.0	357320.0	webin reads Scrambled 2 sample	0:91.50	A:10989624;C:4719485;G:5954777;T:11031603;N:319	91	10989624	4719485	5954777	11031603	319	ERX13611048	ERS22979746	ERA31123310	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19489	19489	ERR14208819	ERX13611039	ERS22979751	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	ythdf2KO 4 sample	SAMEA117628613	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 010\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 010\|scientific name:Danio rerio	Raw reads: ythdf2KO 4 sample	webin reads ythdf2KO 4 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 4 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G09.bam	bam	254231539.0	2766205.0	webin reads ythdf2KO 4 sample	0:91.91	A:63984512;C:40328422;G:86431821;T:63485754;N:1030	91	63984512	40328422	86431821	63485754	1030	ERX13611039	ERS22979751	ERA31123301	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19490	19490	ERR14208808	ERX13611028	ERS22979744	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	GFP 3 sample	SAMEA117628606	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 003\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 003\|scientific name:Danio rerio	Raw reads: GFP 3 sample	webin reads GFP 3 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F03.bam	bam	35932988.0	419944.0	webin reads GFP 3 sample	0:85.57	A:11252929;C:5321445;G:8032297;T:11325814;N:503	85	11252929	5321445	8032297	11325814	503	ERX13611028	ERS22979744	ERA31123290	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19491	19491	ERR14208825	ERX13611045	ERS22979757	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	YTHDF2 2 sample	SAMEA117628619	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 016\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 016\|scientific name:Danio rerio	Raw reads: YTHDF2 2 sample	webin reads YTHDF2 2 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: YTHDF2 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D12.bam	bam	626993184.0	7599502.0	webin reads YTHDF2 2 sample	0:82.50	A:182701108;C:91008174;G:172822143;T:180459253;N:2506	82	182701108	91008174	172822143	180459253	2506	ERX13611045	ERS22979757	ERA31123307	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19492	19492	ERR14208822	ERX13611042	ERS22979756	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	Single cell RNA sequencing of zebrafish heads	YTHDF2 1 sample	SAMEA117628618	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 015\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 015\|scientific name:Danio rerio	Raw reads: YTHDF2 1 sample	webin reads YTHDF2 1 sample		unspecified	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: YTHDF2 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D11.bam	bam	120748751.0	1368887.0	webin reads YTHDF2 1 sample	0:88.21	A:34957526;C:19985010;G:32927086;T:32878659;N:470	88	34957526	19985010	32927086	32878659	470	ERX13611042	ERS22979756	ERA31123304	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
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

Advanced export

JSON shape: default, array, newline-delimited

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");;