{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\" and technology = \"generic-scrnaseq-only\"", "rows": [[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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: Scrambled 1 sample", "webin reads Scrambled 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 2628864, 1112827, 2146146, 2609768, 136, "ERX13611047", "ERS22979745", "ERA31123309", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 1 sample", "webin reads ythdf2KO 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 180836688, 107076381, 193711319, 191586188, 2608, "ERX13611033", "ERS22979748", "ERA31123295", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: GFP 6 sample", "webin reads GFP 6 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 81816649, 55524538, 113686171, 86525390, 1039, "ERX13611031", "ERS22979755", "ERA31123293", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 5 sample", "webin reads ythdf2KO 5 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 56944731, 30766256, 83820146, 55239221, 878, "ERX13611041", "ERS22979752", "ERA31123303", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 3 sample", "webin reads ythdf2KO 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 83933175, 50138103, 128300798, 89051913, 1339, "ERX13611038", "ERS22979750", "ERA31123300", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: YTHDF2 3 sample", "webin reads YTHDF2 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 38910474, 31607688, 67095095, 43403227, 599, "ERX13611046", "ERS22979758", "ERA31123308", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 2 sample", "webin reads ythdf2KO 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 73651155, 41694223, 96485766, 70582706, 982, "ERX13611035", "ERS22979749", "ERA31123297", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: GFP 1 sample", "webin reads GFP 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 2445867, 1074319, 2086526, 2429153, 144, "ERX13611024", "ERS22979742", "ERA31123286", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: Scrambled 3 sample", "webin reads Scrambled 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 30132090, 13700682, 16323331, 29894332, 1079, "ERX13611049", "ERS22979747", "ERA31123311", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: GFP 4 sample", "webin reads GFP 4 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 17589630, 11153310, 25212154, 18323416, 226, "ERX13611029", "ERS22979753", "ERA31123291", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: GFP 2 sample", "webin reads GFP 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 5957309, 2709511, 4434875, 6094552, 345, "ERX13611026", "ERS22979743", "ERA31123288", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: GFP 5 sample", "webin reads GFP 5 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 119077902, 68329173, 126879243, 117420803, 1669, "ERX13611030", "ERS22979754", "ERA31123292", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: Scrambled 2 sample", "webin reads Scrambled 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 10989624, 4719485, 5954777, 11031603, 319, "ERX13611048", "ERS22979746", "ERA31123310", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 4 sample", "webin reads ythdf2KO 4 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 63984512, 40328422, 86431821, 63485754, 1030, "ERX13611039", "ERS22979751", "ERA31123301", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: GFP 3 sample", "webin reads GFP 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 11252929, 5321445, 8032297, 11325814, 503, "ERX13611028", "ERS22979744", "ERA31123290", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: YTHDF2 2 sample", "webin reads YTHDF2 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 182701108, 91008174, 172822143, 180459253, 2506, "ERX13611045", "ERS22979757", "ERA31123307", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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", null, "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", null, null, null, null, null, null, null, null, "Raw reads: YTHDF2 1 sample", "webin reads YTHDF2 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, null, 34957526, 19985010, 32927086, 32878659, 470, "ERX13611042", "ERS22979756", "ERA31123304", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [30691, "SRR28270998", "SRX23880961", "SRS20704477", "SRP494117", "PRJNA1085662", "Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells", "PRJNA1085662", "Other", "Roxithromycin ROX  a commonly used macrolide antibiotic  is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation  ROX persists as a resilient environmental contaminant  detectable in aquatic ecosystems and food products. However  our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study  we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure  particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos  significantly reducing hatch rates  body lengths  and increased malformation rates. Moreover  ROX exposure adversely affected the locomotive capacity of zebrafish embryos  and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons  evident through reduced or irregular axonal lengths. Concurrently  abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax  bcl2  caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1  olig2  axon development cd82a  mbpa  plp1b  sema5a  and neuroimmunity aplnrb  aplnra in zebrafish larvae. Furthermore  the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary  ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.", null, null, null, null, "WT", null, "strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells", "DANIO", "DANIO", "Illumina Second Generation Sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_oligo_dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP494117", null, null, "WT_S1_L001_I1_001.fastq.gz", "fastq", 7991376264.0, 998922033.0, "WT S1 L001 I1 001.fastq.gz", "0:8", "A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175", 8, null, null, null, 2573734851, 1426474966, 1492966198, 2498173074, 27175, "SRX23880961", "SRS20704477", "SRA1820072", "shantou university|Neurobiology Center", "shantou university", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-03-11", "Undetermined", "Multi-stage", "Brain", "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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 247920, 168170, 180799, 203153, 394, "SRX28203119", "SRS24552825", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.E01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 156600, 99183, 113282, 127036, 255, "SRX28203118", "SRS24552823", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.D01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 668634, 393806, 431279, 559022, 1059, "SRX28203117", "SRS24552824", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.C01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 837784, 348085, 463530, 508544, 1109, "SRX28203116", "SRS24552821", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.B01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 1090202, 644484, 702124, 848812, 1886, "SRX28203115", "SRS24552822", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "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.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.G12.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 7", "212", "212", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.F12.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 6", "211", "211", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.D12.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 4", "209", "209", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.C12.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 3", "208", "208", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.B12.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 2", "207", "207", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.A12.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 1", "206", "206", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.H11.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 8", "205", "205", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.G11.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 7", "204", "204", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.F11.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 6", "203", "203", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.E11.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 5", "202", "202", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.D11.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 4", "201", "201", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.G5.fq.gz", null, "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", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 21", "21", "21", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. 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