rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,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.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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