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run_metadata

674 rows where experiment.library_strategy = "RNA-Seq", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "Nervous System"

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experiment.library_selection 4

devstage_curation_coarse 3

devstage_curation 3

tissue_curation 2

experiment.platform 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Nervous System · 674 ✖

technology 1

  • generic-scrnaseq-only · 674 ✖

experiment.library_strategy 1

  • RNA-Seq · 674 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
19221 19221 ERR14935135 ERX14339377 ERS24360099 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H06 Humanized Plate 1 Well H06 SAMEA118225022 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H06|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H06|scientific name:Danio rerio                 Raw reads: Sample HUM1 H06 webin reads Sample HUM1 H06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H06.R1.fastq.gz H06.R2.fastq.gz fastq fastq 168135000.0 560450.0 webin reads Sample HUM1 H06 0:150 1:150 A:49336993;C:19637394;G:50002867;T:49156187;N:1559 150 150     49336993 19637394 50002867 49156187 1559 ERX14339377 ERS24360099 ERA33113052 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19222 19222 ERR14934924 ERX14339166 ERS24360038 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C05 Humanized Plate 1 Well C05 SAMEA118224961 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 C05|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 C05|scientific name:Danio rerio                 Raw reads: Sample HUM1 C05 webin reads Sample HUM1 C05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 C05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C05.R1.fastq.gz C05.R2.fastq.gz fastq fastq 406863000.0 1356210.0 webin reads Sample HUM1 C05 0:150 1:150 A:135043675;C:48707343;G:87607964;T:135501103;N:2915 150 150     135043675 48707343 87607964 135501103 2915 ERX14339166 ERS24360038 ERA33112290 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19223 19223 ERR14934974 ERX14339216 ERS24360047 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D02 Humanized Plate 1 Well D02 SAMEA118224970 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 D02|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 D02|scientific name:Danio rerio                 Raw reads: Sample HUM1 D02 webin reads Sample HUM1 D02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 D02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D02.R1.fastq.gz D02.R2.fastq.gz fastq fastq 231350700.0 771169.0 webin reads Sample HUM1 D02 0:150 1:150 A:61554211;C:27195025;G:82686912;T:59912853;N:1699 150 150     61554211 27195025 82686912 59912853 1699 ERX14339216 ERS24360047 ERA33112492 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19224 19224 ERR14937148 ERX14341392 ERS24422818 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G07 Humanized Plate 2 Well G07 SAMEA118242644 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 G07|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 G07|scientific name:Danio rerio                 Raw reads: Sample HUM2 G07 webin reads Sample HUM2 G07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 G07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G07.R1.fastq.gz G07.R2.fastq.gz fastq fastq 1858827300.0 6196091.0 webin reads Sample HUM2 G07 0:150 1:150 A:377243729;C:275647713;G:834077378;T:371849924;N:8556 150 150     377243729 275647713 834077378 371849924 8556 ERX14341392 ERS24422818 ERA33115718 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19225 19225 ERR14935143 ERX14339385 ERS24360101 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H08 Humanized Plate 1 Well H08 SAMEA118225024 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H08|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H08|scientific name:Danio rerio                 Raw reads: Sample HUM1 H08 webin reads Sample HUM1 H08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H08.R1.fastq.gz H08.R2.fastq.gz fastq fastq 104513100.0 348377.0 webin reads Sample HUM1 H08 0:150 1:150 A:24551652;C:12552824;G:43587381;T:23820238;N:1005 150 150     24551652 12552824 43587381 23820238 1005 ERX14339385 ERS24360101 ERA33113082 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19226 19226 ERR14936904 ERX14341146 ERS24422763 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B12 Humanized Plate 2 Well B12 SAMEA118242589 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 B12|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 B12|scientific name:Danio rerio                 Raw reads: Sample HUM2 B12 webin reads Sample HUM2 B12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 B12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B12.R1.fastq.gz B12.R2.fastq.gz fastq fastq 14783024100.0 49276747.0 webin reads Sample HUM2 B12 0:150 1:150 A:4993941125;C:1900193626;G:3694935207;T:4193880937;N:73205 150 150     4993941125 1900193626 3694935207 4193880937 73205 ERX14341146 ERS24422763 ERA33115587 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19227 19227 ERR14935120 ERX14339362 ERS24360094 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H01 Humanized Plate 1 Well H01 SAMEA118225017 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H01|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H01|scientific name:Danio rerio                 Raw reads: Sample HUM1 H01 webin reads Sample HUM1 H01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H01.R1.fastq.gz H01.R2.fastq.gz fastq fastq 214281900.0 714273.0 webin reads Sample HUM1 H01 0:150 1:150 A:63612930;C:24945238;G:64455038;T:61267490;N:1204 150 150     63612930 24945238 64455038 61267490 1204 ERX14339362 ERS24360094 ERA33112989 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19228 19228 ERR14935021 ERX14339263 ERS24360064 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E07 Humanized Plate 1 Well E07 SAMEA118224987 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 E07|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 E07|scientific name:Danio rerio                 Raw reads: Sample HUM1 E07 webin reads Sample HUM1 E07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 E07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E07.R1.fastq.gz E07.R2.fastq.gz fastq fastq 274863600.0 916212.0 webin reads Sample HUM1 E07 0:150 1:150 A:89634361;C:31803602;G:65721376;T:87702420;N:1841 150 150     89634361 31803602 65721376 87702420 1841 ERX14339263 ERS24360064 ERA33112659 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19229 19229 ERR14950666 ERX14354790 ERS24422897 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C09 Knockout Plate Well C09 SAMEA118242723 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO C09|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO C09|scientific name:Danio rerio                 Raw reads: Sample KO C09 webin reads Sample KO C09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO C09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C09.R1.fastq.gz C09.R2.fastq.gz fastq fastq 12910892700.0 43036309.0 webin reads Sample KO C09 0:150 1:150 A:4656205100;C:1791783755;G:2065221420;T:4397579948;N:102477 150 150     4656205100 1791783755 2065221420 4397579948 102477 ERX14354790 ERS24422897 ERA33121161 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19230 19230 ERR14936878 ERX14341120 ERS24422755 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B04 Humanized Plate 2 Well B04 SAMEA118242581 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 B04|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 B04|scientific name:Danio rerio                 Raw reads: Sample HUM2 B04 webin reads Sample HUM2 B04   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 B04 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B04.R1.fastq.gz B04.R2.fastq.gz fastq fastq 2614344300.0 8714481.0 webin reads Sample HUM2 B04 0:150 1:150 A:495532634;C:388504084;G:1222436337;T:507858943;N:12302 150 150     495532634 388504084 1222436337 507858943 12302 ERX14341120 ERS24422755 ERA33115558 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19231 19231 ERR14950561 ERX14354685 ERS24422871 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A07 Knockout Plate Well A07 SAMEA118242697 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO A07|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO A07|scientific name:Danio rerio                 Raw reads: Sample KO A07 webin reads Sample KO A07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO A07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A07.R1.fastq.gz A07.R2.fastq.gz fastq fastq 3401128800.0 11337096.0 webin reads Sample KO A07 0:150 1:150 A:1234869505;C:459023584;G:579824655;T:1127383390;N:27666 150 150     1234869505 459023584 579824655 1127383390 27666 ERX14354685 ERS24422871 ERA33121056 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19232 19232 ERR14936823 ERX14341065 ERS24422746 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A07 Humanized Plate 2 Well A07 SAMEA118242572 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 A07|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 A07|scientific name:Danio rerio                 Raw reads: Sample HUM2 A07 webin reads Sample HUM2 A07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 A07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A07.R1.fastq.gz A07.R2.fastq.gz fastq fastq 3778502100.0 12595007.0 webin reads Sample HUM2 A07 0:150 1:150 A:710336891;C:494217522;G:1880968771;T:692961837;N:17079 150 150     710336891 494217522 1880968771 692961837 17079 ERX14341065 ERS24422746 ERA33115511 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19233 19233 ERR14937143 ERX14341387 ERS24422813 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G02 Humanized Plate 2 Well G02 SAMEA118242639 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 G02|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 G02|scientific name:Danio rerio                 Raw reads: Sample HUM2 G02 webin reads Sample HUM2 G02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 G02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G02.R1.fastq.gz G02.R2.fastq.gz fastq fastq 5962135800.0 19873786.0 webin reads Sample HUM2 G02 0:150 1:150 A:1745436521;C:821720129;G:1863789129;T:1531162608;N:27413 150 150     1745436521 821720129 1863789129 1531162608 27413 ERX14341387 ERS24422813 ERA33115710 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19234 19234 ERR14934810 ERX14339052 ERS24360011 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A02 Humanized Plate 1 Well A02 SAMEA118224934 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A02|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A02|scientific name:Danio rerio                 Raw reads: Sample HUM1 A02 webin reads Sample HUM1 A02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A02.R1.fastq.gz A02.R2.fastq.gz fastq fastq 480559200.0 1601864.0 webin reads Sample HUM1 A02 0:150 1:150 A:163177108;C:53718756;G:98835089;T:164825485;N:2762 150 150     163177108 53718756 98835089 164825485 2762 ERX14339052 ERS24360011 ERA33111955 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19235 19235 ERR14934984 ERX14339226 ERS24360049 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D04 Humanized Plate 1 Well D04 SAMEA118224972 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 D04|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 D04|scientific name:Danio rerio                 Raw reads: Sample HUM1 D04 webin reads Sample HUM1 D04   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 D04 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D04.R1.fastq.gz D04.R2.fastq.gz fastq fastq 179225700.0 597419.0 webin reads Sample HUM1 D04 0:150 1:150 A:45457519;C:22876690;G:67395901;T:43493765;N:1825 150 150     45457519 22876690 67395901 43493765 1825 ERX14339226 ERS24360049 ERA33112537 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19236 19236 ERR14934845 ERX14339087 ERS24360021 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A12 Humanized Plate 1 Well A12 SAMEA118224944 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A12|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A12|scientific name:Danio rerio                 Raw reads: Sample HUM1 A12 webin reads Sample HUM1 A12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A12.R1.fastq.gz A12.R2.fastq.gz fastq fastq 77425200.0 258084.0 webin reads Sample HUM1 A12 0:150 1:150 A:16644810;C:10391814;G:34720928;T:15667259;N:389 150 150     16644810 10391814 34720928 15667259 389 ERX14339087 ERS24360021 ERA33112104 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19237 19237 ERR14934855 ERX14339097 ERS24360024 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B03 Humanized Plate 1 Well B03 SAMEA118224947 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B03|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B03|scientific name:Danio rerio                 Raw reads: Sample HUM1 B03 webin reads Sample HUM1 B03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B03.R1.fastq.gz B03.R2.fastq.gz fastq fastq 94155000.0 313850.0 webin reads Sample HUM1 B03 0:150 1:150 A:23101292;C:11479599;G:38484223;T:21089074;N:812 150 150     23101292 11479599 38484223 21089074 812 ERX14339097 ERS24360024 ERA33112137 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19238 19238 ERR14943975 ERX14348127 ERS24422869 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A05 Knockout Plate Well A05 SAMEA118242695 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO A05|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO A05|scientific name:Danio rerio                 Raw reads: Sample KO A05 webin reads Sample KO A05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO A05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A05.R1.fastq.gz A05.R2.fastq.gz fastq fastq 3911878200.0 13039594.0 webin reads Sample KO A05 0:150 1:150 A:1402938003;C:529582691;G:715316068;T:1264010327;N:31111 150 150     1402938003 529582691 715316068 1264010327 31111 ERX14348127 ERS24422869 ERA33119600 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19239 19239 ERR14937117 ERX14341361 ERS24422810 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F11 Humanized Plate 2 Well F11 SAMEA118242636 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 F11|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 F11|scientific name:Danio rerio                 Raw reads: Sample HUM2 F11 webin reads Sample HUM2 F11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 F11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F11.R1.fastq.gz F11.R2.fastq.gz fastq fastq 3943764300.0 13145881.0 webin reads Sample HUM2 F11 0:150 1:150 A:1194917338;C:577472498;G:1192413538;T:978942667;N:18259 150 150     1194917338 577472498 1192413538 978942667 18259 ERX14341361 ERS24422810 ERA33115700 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19240 19240 ERR14935149 ERX14339391 ERS24360104 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H11 Humanized Plate 1 Well H11 SAMEA118225027 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H11|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H11|scientific name:Danio rerio                 Raw reads: Sample HUM1 H11 webin reads Sample HUM1 H11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H11.R1.fastq.gz H11.R2.fastq.gz fastq fastq 29087400.0 96958.0 webin reads Sample HUM1 H11 0:150 1:150 A:5335277;C:3932942;G:14621885;T:5197119;N:177 150 150     5335277 3932942 14621885 5197119 177 ERX14339391 ERS24360104 ERA33113103 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19241 19241 ERR14935025 ERX14339267 ERS24360065 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E08 Humanized Plate 1 Well E08 SAMEA118224988 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 E08|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 E08|scientific name:Danio rerio                 Raw reads: Sample HUM1 E08 webin reads Sample HUM1 E08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 E08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E08.R1.fastq.gz E08.R2.fastq.gz fastq fastq 220002300.0 733341.0 webin reads Sample HUM1 E08 0:150 1:150 A:62013327;C:25647839;G:72394925;T:59944865;N:1344 150 150     62013327 25647839 72394925 59944865 1344 ERX14339267 ERS24360065 ERA33112670 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19242 19242 ERR14935108 ERX14339350 ERS24360090 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G09 Humanized Plate 1 Well G09 SAMEA118225013 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 G09|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 G09|scientific name:Danio rerio                 Raw reads: Sample HUM1 G09 webin reads Sample HUM1 G09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 G09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G09.R1.fastq.gz G09.R2.fastq.gz fastq fastq 55286400.0 184288.0 webin reads Sample HUM1 G09 0:150 1:150 A:9253015;C:6978214;G:29393822;T:9661042;N:307 150 150     9253015 6978214 29393822 9661042 307 ERX14339350 ERS24360090 ERA33112953 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19243 19243 ERR14935106 ERX14339348 ERS24360089 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G08 Humanized Plate 1 Well G08 SAMEA118225012 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 G08|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 G08|scientific name:Danio rerio                 Raw reads: Sample HUM1 G08 webin reads Sample HUM1 G08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 G08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G08.R1.fastq.gz G08.R2.fastq.gz fastq fastq 90390000.0 301300.0 webin reads Sample HUM1 G08 0:150 1:150 A:14519869;C:11004100;G:49374862;T:15490478;N:691 150 150     14519869 11004100 49374862 15490478 691 ERX14339348 ERS24360089 ERA33112948 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19244 19244 ERR14934877 ERX14339119 ERS24360032 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B11 Humanized Plate 1 Well B11 SAMEA118224955 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B11|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B11|scientific name:Danio rerio                 Raw reads: Sample HUM1 B11 webin reads Sample HUM1 B11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B11.R1.fastq.gz B11.R2.fastq.gz fastq fastq 99908700.0 333029.0 webin reads Sample HUM1 B11 0:150 1:150 A:22260827;C:11949991;G:42744522;T:22952623;N:737 150 150     22260827 11949991 42744522 22952623 737 ERX14339119 ERS24360032 ERA33112207 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19245 19245 ERR14934885 ERX14339127 ERS24360034 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C01 Humanized Plate 1 Well C01 SAMEA118224957 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 C01|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 C01|scientific name:Danio rerio                 Raw reads: Sample HUM1 C01 webin reads Sample HUM1 C01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 C01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C01.R1.fastq.gz C01.R2.fastq.gz fastq fastq 101124300.0 337081.0 webin reads Sample HUM1 C01 0:150 1:150 A:21597244;C:13549354;G:45547786;T:20429406;N:510 150 150     21597244 13549354 45547786 20429406 510 ERX14339127 ERS24360034 ERA33112235 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19246 19246 ERR14943984 ERX14348136 ERS24422880 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B04 Knockout Plate Well B04 SAMEA118242706 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO B04|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO B04|scientific name:Danio rerio                 Raw reads: Sample KO B04 webin reads Sample KO B04   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO B04 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B04.R1.fastq.gz B04.R2.fastq.gz fastq fastq 561237900.0 1870793.0 webin reads Sample KO B04 0:150 1:150 A:192169170;C:77013107;G:120338699;T:171712356;N:4568 150 150     192169170 77013107 120338699 171712356 4568 ERX14348136 ERS24422880 ERA33119691 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19247 19247 ERR14938992 ERX14343236 ERS24422834 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H11 Humanized Plate 2 Well H11 SAMEA118242660 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 H11|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 H11|scientific name:Danio rerio                 Raw reads: Sample HUM2 H11 webin reads Sample HUM2 H11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 H11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H11.R1.fastq.gz H11.R2.fastq.gz fastq fastq 1733814900.0 5779383.0 webin reads Sample HUM2 H11 0:150 1:150 A:378393702;C:284557462;G:721428373;T:349427441;N:7922 150 150     378393702 284557462 721428373 349427441 7922 ERX14343236 ERS24422834 ERA33115755 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19248 19248 ERR14937159 ERX14341403 ERS24422829 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H06 Humanized Plate 2 Well H06 SAMEA118242655 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 H06|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 H06|scientific name:Danio rerio                 Raw reads: Sample HUM2 H06 webin reads Sample HUM2 H06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 H06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H06.R1.fastq.gz H06.R2.fastq.gz fastq fastq 8840167200.0 29467224.0 webin reads Sample HUM2 H06 0:150 1:150 A:3070163952;C:1202397032;G:1876790493;T:2690771671;N:44052 150 150     3070163952 1202397032 1876790493 2690771671 44052 ERX14341403 ERS24422829 ERA33115733 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19249 19249 ERR14934852 ERX14339094 ERS24360023 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B02 Humanized Plate 1 Well B02 SAMEA118224946 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B02|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B02|scientific name:Danio rerio                 Raw reads: Sample HUM1 B02 webin reads Sample HUM1 B02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B02.R1.fastq.gz B02.R2.fastq.gz fastq fastq 123106800.0 410356.0 webin reads Sample HUM1 B02 0:150 1:150 A:24870369;C:15859782;G:60046944;T:22329104;N:601 150 150     24870369 15859782 60046944 22329104 601 ERX14339094 ERS24360023 ERA33112126 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19250 19250 ERR14936902 ERX14341144 ERS24422761 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B10 Humanized Plate 2 Well B10 SAMEA118242587 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 B10|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 B10|scientific name:Danio rerio                 Raw reads: Sample HUM2 B10 webin reads Sample HUM2 B10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 B10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B10.R1.fastq.gz B10.R2.fastq.gz fastq fastq 3818756100.0 12729187.0 webin reads Sample HUM2 B10 0:150 1:150 A:801009311;C:582803669;G:1691856038;T:743070146;N:16936 150 150     801009311 582803669 1691856038 743070146 16936 ERX14341144 ERS24422761 ERA33115582 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19251 19251 ERR14935145 ERX14339387 ERS24360102 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H09 Humanized Plate 1 Well H09 SAMEA118225025 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H09|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H09|scientific name:Danio rerio                 Raw reads: Sample HUM1 H09 webin reads Sample HUM1 H09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H09.R1.fastq.gz H09.R2.fastq.gz fastq fastq 79435500.0 264785.0 webin reads Sample HUM1 H09 0:150 1:150 A:19325284;C:9616771;G:32084598;T:18408162;N:685 150 150     19325284 9616771 32084598 18408162 685 ERX14339387 ERS24360102 ERA33113089 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19252 19252 ERR14935006 ERX14339248 ERS24360059 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E02 Humanized Plate 1 Well E02 SAMEA118224982 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 E02|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 E02|scientific name:Danio rerio                 Raw reads: Sample HUM1 E02 webin reads Sample HUM1 E02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 E02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E02.R1.fastq.gz E02.R2.fastq.gz fastq fastq 184473600.0 614912.0 webin reads Sample HUM1 E02 0:150 1:150 A:47275758;C:21941025;G:68635035;T:46620684;N:1098 150 150     47275758 21941025 68635035 46620684 1098 ERX14339248 ERS24360059 ERA33112606 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19253 19253 ERR14937114 ERX14341358 ERS24422807 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F08 Humanized Plate 2 Well F08 SAMEA118242633 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 F08|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 F08|scientific name:Danio rerio                 Raw reads: Sample HUM2 F08 webin reads Sample HUM2 F08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 F08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F08.R1.fastq.gz F08.R2.fastq.gz fastq fastq 5604971400.0 18683238.0 webin reads Sample HUM2 F08 0:150 1:150 A:1272096391;C:927796029;G:2253030240;T:1152025287;N:23453 150 150     1272096391 927796029 2253030240 1152025287 23453 ERX14341358 ERS24422807 ERA33115697 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19254 19254 ERR14935115 ERX14339357 ERS24360092 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G11 Humanized Plate 1 Well G11 SAMEA118225015 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 G11|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 G11|scientific name:Danio rerio                 Raw reads: Sample HUM1 G11 webin reads Sample HUM1 G11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 G11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G11.R1.fastq.gz G11.R2.fastq.gz fastq fastq 18225600.0 60752.0 webin reads Sample HUM1 G11 0:150 1:150 A:3396385;C:2248165;G:9171340;T:3409593;N:117 150 150     3396385 2248165 9171340 3409593 117 ERX14339357 ERS24360092 ERA33112973 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19255 19255 ERR14950748 ERX14354872 ERS24422916 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F01 Knockout Plate Well F01 SAMEA118242742 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO F01|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO F01|scientific name:Danio rerio                 Raw reads: Sample KO F01 webin reads Sample KO F01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO F01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F01.R1.fastq.gz F01.R2.fastq.gz fastq fastq 3161931900.0 10539773.0 webin reads Sample KO F01 0:150 1:150 A:1111325789;C:460593692;G:495389420;T:1094598021;N:24978 150 150     1111325789 460593692 495389420 1094598021 24978 ERX14354872 ERS24422916 ERA33121243 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19256 19256 ERR14934881 ERX14339123 ERS24360033 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B12 Humanized Plate 1 Well B12 SAMEA118224956 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B12|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B12|scientific name:Danio rerio                 Raw reads: Sample HUM1 B12 webin reads Sample HUM1 B12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B12.R1.fastq.gz B12.R2.fastq.gz fastq fastq 116537700.0 388459.0 webin reads Sample HUM1 B12 0:150 1:150 A:27658956;C:13844738;G:48483886;T:26549255;N:865 150 150     27658956 13844738 48483886 26549255 865 ERX14339123 ERS24360033 ERA33112224 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19257 19257 ERR14934824 ERX14339066 ERS24360013 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A04 Humanized Plate 1 Well A04 SAMEA118224936 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A04|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A04|scientific name:Danio rerio                 Raw reads: Sample HUM1 A04 webin reads Sample HUM1 A04   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A04 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A04.R1.fastq.gz A04.R2.fastq.gz fastq fastq 190861200.0 636204.0 webin reads Sample HUM1 A04 0:150 1:150 A:51866429;C:22469460;G:65825429;T:50698008;N:1874 150 150     51866429 22469460 65825429 50698008 1874 ERX14339066 ERS24360013 ERA33112023 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19258 19258 ERR14934950 ERX14339192 ERS24360041 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C08 Humanized Plate 1 Well C08 SAMEA118224964 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 C08|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 C08|scientific name:Danio rerio                 Raw reads: Sample HUM1 C08 webin reads Sample HUM1 C08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 C08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C08.R1.fastq.gz C08.R2.fastq.gz fastq fastq 347655600.0 1158852.0 webin reads Sample HUM1 C08 0:150 1:150 A:111273717;C:41410769;G:81188146;T:113779846;N:3122 150 150     111273717 41410769 81188146 113779846 3122 ERX14339192 ERS24360041 ERA33112408 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19259 19259 ERR14936959 ERX14341201 ERS24422772 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C09 Humanized Plate 2 Well C09 SAMEA118242598 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 C09|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 C09|scientific name:Danio rerio                 Raw reads: Sample HUM2 C09 webin reads Sample HUM2 C09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 C09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C09.R1.fastq.gz C09.R2.fastq.gz fastq fastq 3716150400.0 12387168.0 webin reads Sample HUM2 C09 0:150 1:150 A:950093356;C:589554852;G:1341746189;T:834739539;N:16464 150 150     950093356 589554852 1341746189 834739539 16464 ERX14341201 ERS24422772 ERA33115600 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19260 19260 ERR14934954 ERX14339196 ERS24360042 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C09 Humanized Plate 1 Well C09 SAMEA118224965 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 C09|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 C09|scientific name:Danio rerio                 Raw reads: Sample HUM1 C09 webin reads Sample HUM1 C09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 C09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C09.R1.fastq.gz C09.R2.fastq.gz fastq fastq 160752900.0 535843.0 webin reads Sample HUM1 C09 0:150 1:150 A:47408978;C:19223052;G:47019288;T:47100126;N:1456 150 150     47408978 19223052 47019288 47100126 1456 ERX14339196 ERS24360042 ERA33112423 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19261 19261 ERR14950615 ERX14354739 ERS24422889 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C01 Knockout Plate Well C01 SAMEA118242715 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO C01|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO C01|scientific name:Danio rerio                 Raw reads: Sample KO C01 webin reads Sample KO C01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO C01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C01.R1.fastq.gz C01.R2.fastq.gz fastq fastq 12926966100.0 43089887.0 webin reads Sample KO C01 0:150 1:150 A:4670066457;C:1792574588;G:2068594468;T:4395628669;N:101918 150 150     4670066457 1792574588 2068594468 4395628669 101918 ERX14354739 ERS24422889 ERA33121110 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19262 19262 ERR14950602 ERX14354726 ERS24422887 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B11 Knockout Plate Well B11 SAMEA118242713 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO B11|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO B11|scientific name:Danio rerio                 Raw reads: Sample KO B11 webin reads Sample KO B11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO B11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B11.R1.fastq.gz B11.R2.fastq.gz fastq fastq 7240824000.0 24136080.0 webin reads Sample KO B11 0:150 1:150 A:2670219676;C:931192972;G:1216106261;T:2423246169;N:58922 150 150     2670219676 931192972 1216106261 2423246169 58922 ERX14354726 ERS24422887 ERA33121097 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19263 19263 ERR14950677 ERX14354801 ERS24422900 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C12 Knockout Plate Well C12 SAMEA118242726 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO C12|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO C12|scientific name:Danio rerio                 Raw reads: Sample KO C12 webin reads Sample KO C12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO C12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C12.R1.fastq.gz C12.R2.fastq.gz fastq fastq 8490801000.0 28302670.0 webin reads Sample KO C12 0:150 1:150 A:3049316720;C:1192674579;G:1458160432;T:2790581120;N:68149 150 150     3049316720 1192674579 1458160432 2790581120 68149 ERX14354801 ERS24422900 ERA33121172 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19264 19264 ERR14950597 ERX14354721 ERS24422886 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B10 Knockout Plate Well B10 SAMEA118242712 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO B10|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO B10|scientific name:Danio rerio                 Raw reads: Sample KO B10 webin reads Sample KO B10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO B10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B10.R1.fastq.gz B10.R2.fastq.gz fastq fastq 9344290800.0 31147636.0 webin reads Sample KO B10 0:150 1:150 A:3401103081;C:1284404735;G:1572646132;T:3086062190;N:74662 150 150     3401103081 1284404735 1572646132 3086062190 74662 ERX14354721 ERS24422886 ERA33121092 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19265 19265 ERR14950734 ERX14354858 ERS24422911 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E08 Knockout Plate Well E08 SAMEA118242737 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO E08|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO E08|scientific name:Danio rerio                 Raw reads: Sample KO E08 webin reads Sample KO E08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO E08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E08.R1.fastq.gz E08.R2.fastq.gz fastq fastq 1843996200.0 6146654.0 webin reads Sample KO E08 0:150 1:150 A:639221474;C:243164058;G:390761341;T:570834581;N:14746 150 150     639221474 243164058 390761341 570834581 14746 ERX14354858 ERS24422911 ERA33121229 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19266 19266 ERR14943982 ERX14348134 ERS24422877 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B01 Knockout Plate Well B01 SAMEA118242703 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO B01|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO B01|scientific name:Danio rerio                 Raw reads: Sample KO B01 webin reads Sample KO B01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO B01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B01.R1.fastq.gz B01.R2.fastq.gz fastq fastq 11318469900.0 37728233.0 webin reads Sample KO B01 0:150 1:150 A:4086308197;C:1546883485;G:1844189302;T:3841000200;N:88716 150 150     4086308197 1546883485 1844189302 3841000200 88716 ERX14348134 ERS24422877 ERA33119688 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19267 19267 ERR14950636 ERX14354760 ERS24422893 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C05 Knockout Plate Well C05 SAMEA118242719 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO C05|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO C05|scientific name:Danio rerio                 Raw reads: Sample KO C05 webin reads Sample KO C05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO C05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C05.R2.fastq.gz C05.R1.fastq.gz fastq fastq 13861467300.0 46204891.0 webin reads Sample KO C05 0:150 1:150 A:4748497970;C:2174952613;G:2309004592;T:4628898110;N:114015 150 150     4748497970 2174952613 2309004592 4628898110 114015 ERX14354760 ERS24422893 ERA33121131 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19268 19268 ERR14935064 ERX14339306 ERS24360078 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F09 Humanized Plate 1 Well F09 SAMEA118225001 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 F09|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 F09|scientific name:Danio rerio                 Raw reads: Sample HUM1 F09 webin reads Sample HUM1 F09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 F09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F09.R1.fastq.gz F09.R2.fastq.gz fastq fastq 393873600.0 1312912.0 webin reads Sample HUM1 F09 0:150 1:150 A:125159366;C:49326024;G:94522011;T:124863337;N:2862 150 150     125159366 49326024 94522011 124863337 2862 ERX14339306 ERS24360078 ERA33112801 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19269 19269 ERR14934858 ERX14339100 ERS24360025 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B04 Humanized Plate 1 Well B04 SAMEA118224948 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B04|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B04|scientific name:Danio rerio                 Raw reads: Sample HUM1 B04 webin reads Sample HUM1 B04   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B04 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B04.R1.fastq.gz B04.R2.fastq.gz fastq fastq 85698600.0 285662.0 webin reads Sample HUM1 B04 0:150 1:150 A:16127871;C:10936313;G:42563818;T:16070081;N:517 150 150     16127871 10936313 42563818 16070081 517 ERX14339100 ERS24360025 ERA33112146 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19270 19270 ERR14950548 ERX14354672 ERS24422866 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A02 Knockout Plate Well A02 SAMEA118242692 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO A02|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO A02|scientific name:Danio rerio                 Raw reads: Sample KO A02 webin reads Sample KO A02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO A02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A02.R1.fastq.gz A02.R2.fastq.gz fastq fastq 3357020700.0 11190069.0 webin reads Sample KO A02 0:150 1:150 A:1198525901;C:478732184;G:572930834;T:1106804630;N:27151 150 150     1198525901 478732184 572930834 1106804630 27151 ERX14354672 ERS24422866 ERA33121043 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19271 19271 ERR14936843 ERX14341085 ERS24422751 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A12 Humanized Plate 2 Well A12 SAMEA118242577 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 A12|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 A12|scientific name:Danio rerio                 Raw reads: Sample HUM2 A12 webin reads Sample HUM2 A12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 A12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A12.R1.fastq.gz A12.R2.fastq.gz fastq fastq 10256706300.0 34189021.0 webin reads Sample HUM2 A12 0:150 1:150 A:3536584478;C:1403340948;G:2397966213;T:2918763136;N:51525 150 150     3536584478 1403340948 2397966213 2918763136 51525 ERX14341085 ERS24422751 ERA33115534 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19272 19272 ERR14950795 ERX14354919 ERS24422930 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G03 Knockout Plate Well G03 SAMEA118242756 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO G03|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO G03|scientific name:Danio rerio                 Raw reads: Sample KO G03 webin reads Sample KO G03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO G03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G03.R1.fastq.gz G03.R2.fastq.gz fastq fastq 7364946000.0 24549820.0 webin reads Sample KO G03 0:150 1:150 A:2672614853;C:1036322394;G:1247472746;T:2408476880;N:59127 150 150     2672614853 1036322394 1247472746 2408476880 59127 ERX14354919 ERS24422930 ERA33121291 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19273 19273 ERR14935029 ERX14339271 ERS24360067 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E10 Humanized Plate 1 Well E10 SAMEA118224990 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 E10|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 E10|scientific name:Danio rerio                 Raw reads: Sample HUM1 E10 webin reads Sample HUM1 E10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 E10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E10.R1.fastq.gz E10.R2.fastq.gz fastq fastq 137180100.0 457267.0 webin reads Sample HUM1 E10 0:150 1:150 A:33764068;C:16452119;G:53129173;T:33833524;N:1216 150 150     33764068 16452119 53129173 33833524 1216 ERX14339271 ERS24360067 ERA33112682 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19274 19274 ERR14937113 ERX14341357 ERS24422806 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F07 Humanized Plate 2 Well F07 SAMEA118242632 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 F07|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 F07|scientific name:Danio rerio                 Raw reads: Sample HUM2 F07 webin reads Sample HUM2 F07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 F07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F07.R1.fastq.gz F07.R2.fastq.gz fastq fastq 3764933100.0 12549777.0 webin reads Sample HUM2 F07 0:150 1:150 A:931279746;C:549119528;G:1391605324;T:892911306;N:17196 150 150     931279746 549119528 1391605324 892911306 17196 ERX14341357 ERS24422806 ERA33115695 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19275 19275 ERR14952973 ERX14357127 ERS24422835 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H12 Humanized Plate 2 Well H12 SAMEA118242661 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 H12|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 H12|scientific name:Danio rerio                 Raw reads: Sample HUM2 H12 webin reads Sample HUM2 H12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 H12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H12.R1.fastq.gz H12.R2.fastq.gz fastq fastq 4110320400.0 13701068.0 webin reads Sample HUM2 H12 0:150 1:150 A:994038023;C:659909232;G:1578428805;T:877925810;N:18530 150 150     994038023 659909232 1578428805 877925810 18530 ERX14357127 ERS24422835 ERA33122913 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19276 19276 ERR14935019 ERX14339261 ERS24360063 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E06 Humanized Plate 1 Well E06 SAMEA118224986 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 E06|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 E06|scientific name:Danio rerio                 Raw reads: Sample HUM1 E06 webin reads Sample HUM1 E06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 E06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E06.R1.fastq.gz E06.R2.fastq.gz fastq fastq 250613700.0 835379.0 webin reads Sample HUM1 E06 0:150 1:150 A:75679048;C:30156356;G:70614639;T:74161729;N:1928 150 150     75679048 30156356 70614639 74161729 1928 ERX14339261 ERS24360063 ERA33112650 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19277 19277 ERR14937144 ERX14341388 ERS24422814 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G03 Humanized Plate 2 Well G03 SAMEA118242640 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 G03|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 G03|scientific name:Danio rerio                 Raw reads: Sample HUM2 G03 webin reads Sample HUM2 G03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 G03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G03.R1.fastq.gz G03.R2.fastq.gz fastq fastq 4967196600.0 16557322.0 webin reads Sample HUM2 G03 0:150 1:150 A:1310441558;C:730142812;G:1820047798;T:1106541425;N:23007 150 150     1310441558 730142812 1820047798 1106541425 23007 ERX14341388 ERS24422814 ERA33115713 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19278 19278 ERR14936818 ERX14341060 ERS24422741 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A02 Humanized Plate 2 Well A02 SAMEA118242567 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 A02|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 A02|scientific name:Danio rerio                 Raw reads: Sample HUM2 A02 webin reads Sample HUM2 A02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 A02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A02.R1.fastq.gz A02.R2.fastq.gz fastq fastq 3217733700.0 10725779.0 webin reads Sample HUM2 A02 0:150 1:150 A:686575330;C:510490874;G:1381211600;T:639440992;N:14904 150 150     686575330 510490874 1381211600 639440992 14904 ERX14341060 ERS24422741 ERA33115505 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19279 19279 ERR14950774 ERX14354898 ERS24422922 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F07 Knockout Plate Well F07 SAMEA118242748 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO F07|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO F07|scientific name:Danio rerio                 Raw reads: Sample KO F07 webin reads Sample KO F07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO F07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F07.R1.fastq.gz F07.R2.fastq.gz fastq fastq 10763253300.0 35877511.0 webin reads Sample KO F07 0:150 1:150 A:3904704604;C:1492936538;G:1705278852;T:3660244628;N:88678 150 150     3904704604 1492936538 1705278852 3660244628 88678 ERX14354898 ERS24422922 ERA33121270 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19280 19280 ERR14934968 ERX14339210 ERS24360046 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D01 Humanized Plate 1 Well D01 SAMEA118224969 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 D01|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 D01|scientific name:Danio rerio                 Raw reads: Sample HUM1 D01 webin reads Sample HUM1 D01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 D01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D01.R1.fastq.gz D01.R2.fastq.gz fastq fastq 169613700.0 565379.0 webin reads Sample HUM1 D01 0:150 1:150 A:44186025;C:22437297;G:59635089;T:43353786;N:1503 150 150     44186025 22437297 59635089 43353786 1503 ERX14339210 ERS24360046 ERA33112474 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19281 19281 ERR14944006 ERX14348158 ERS24422884 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B08 Knockout Plate Well B08 SAMEA118242710 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO B08|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO B08|scientific name:Danio rerio                 Raw reads: Sample KO B08 webin reads Sample KO B08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO B08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B08.R1.fastq.gz B08.R2.fastq.gz fastq fastq 4374918300.0 14583061.0 webin reads Sample KO B08 0:150 1:150 A:1502989289;C:608306022;G:868547831;T:1395039881;N:35277 150 150     1502989289 608306022 868547831 1395039881 35277 ERX14348158 ERS24422884 ERA33119742 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19282 19282 ERR14935068 ERX14339310 ERS24360079 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F10 Humanized Plate 1 Well F10 SAMEA118225002 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 F10|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 F10|scientific name:Danio rerio                 Raw reads: Sample HUM1 F10 webin reads Sample HUM1 F10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 F10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F10.R1.fastq.gz F10.R2.fastq.gz fastq fastq 366521100.0 1221737.0 webin reads Sample HUM1 F10 0:150 1:150 A:120362548;C:43174281;G:81935740;T:121045446;N:3085 150 150     120362548 43174281 81935740 121045446 3085 ERX14339310 ERS24360079 ERA33112816 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19283 19283 ERR14935151 ERX14339393 ERS24360105 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H12 Humanized Plate 1 Well H12 SAMEA118225028 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H12|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H12|scientific name:Danio rerio                 Raw reads: Sample HUM1 H12 webin reads Sample HUM1 H12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H12.R1.fastq.gz H12.R2.fastq.gz fastq fastq 64716600.0 215722.0 webin reads Sample HUM1 H12 0:150 1:150 A:11919103;C:8780603;G:32437007;T:11579359;N:528 150 150     11919103 8780603 32437007 11579359 528 ERX14339393 ERS24360105 ERA33113116 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19284 19284 ERR14950775 ERX14354899 ERS24422923 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F08 Knockout Plate Well F08 SAMEA118242749 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO F08|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO F08|scientific name:Danio rerio                 Raw reads: Sample KO F08 webin reads Sample KO F08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO F08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F08.R1.fastq.gz F08.R2.fastq.gz fastq fastq 862013100.0 2873377.0 webin reads Sample KO F08 0:150 1:150 A:258529164;C:123157615;G:260317379;T:220001971;N:6971 150 150     258529164 123157615 260317379 220001971 6971 ERX14354899 ERS24422923 ERA33121271 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19285 19285 ERR14934987 ERX14339229 ERS24360050 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D05 Humanized Plate 1 Well D05 SAMEA118224973 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 D05|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 D05|scientific name:Danio rerio                 Raw reads: Sample HUM1 D05 webin reads Sample HUM1 D05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 D05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D05.R1.fastq.gz D05.R2.fastq.gz fastq fastq 87887400.0 292958.0 webin reads Sample HUM1 D05 0:150 1:150 A:19996165;C:11416204;G:37562812;T:18911751;N:468 150 150     19996165 11416204 37562812 18911751 468 ERX14339229 ERS24360050 ERA33112543 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19286 19286 ERR14950668 ERX14354792 ERS24422898 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C10 Knockout Plate Well C10 SAMEA118242724 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO C10|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO C10|scientific name:Danio rerio                 Raw reads: Sample KO C10 webin reads Sample KO C10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO C10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C10.R1.fastq.gz C10.R2.fastq.gz fastq fastq 2650018500.0 8833395.0 webin reads Sample KO C10 0:150 1:150 A:944147055;C:380161906;G:445871150;T:879817280;N:21109 150 150     944147055 380161906 445871150 879817280 21109 ERX14354792 ERS24422898 ERA33121163 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19287 19287 ERR14937108 ERX14341352 ERS24422801 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F02 Humanized Plate 2 Well F02 SAMEA118242627 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 F02|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 F02|scientific name:Danio rerio                 Raw reads: Sample HUM2 F02 webin reads Sample HUM2 F02   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 F02 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F02.R1.fastq.gz F02.R2.fastq.gz fastq fastq 4319451600.0 14398172.0 webin reads Sample HUM2 F02 0:150 1:150 A:1013913720;C:720345672;G:1637113325;T:948057846;N:21037 150 150     1013913720 720345672 1637113325 948057846 21037 ERX14341352 ERS24422801 ERA33115690 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19288 19288 ERR14934840 ERX14339082 ERS24360019 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A10 Humanized Plate 1 Well A10 SAMEA118224942 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A10|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A10|scientific name:Danio rerio                 Raw reads: Sample HUM1 A10 webin reads Sample HUM1 A10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A10.R1.fastq.gz A10.R2.fastq.gz fastq fastq 55647900.0 185493.0 webin reads Sample HUM1 A10 0:150 1:150 A:8450799;C:7127607;G:31284165;T:8784914;N:415 150 150     8450799 7127607 31284165 8784914 415 ERX14339082 ERS24360019 ERA33112084 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19289 19289 ERR14935132 ERX14339374 ERS24360098 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H05 Humanized Plate 1 Well H05 SAMEA118225021 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 H05|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 H05|scientific name:Danio rerio                 Raw reads: Sample HUM1 H05 webin reads Sample HUM1 H05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 H05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H05.R1.fastq.gz H05.R2.fastq.gz fastq fastq 161532600.0 538442.0 webin reads Sample HUM1 H05 0:150 1:150 A:46954082;C:18456156;G:50213476;T:45907368;N:1518 150 150     46954082 18456156 50213476 45907368 1518 ERX14339374 ERS24360098 ERA33113034 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19290 19290 ERR14934993 ERX14339235 ERS24360053 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D08 Humanized Plate 1 Well D08 SAMEA118224976 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 D08|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 D08|scientific name:Danio rerio                 Raw reads: Sample HUM1 D08 webin reads Sample HUM1 D08   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 D08 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D08.R1.fastq.gz D08.R2.fastq.gz fastq fastq 163574400.0 545248.0 webin reads Sample HUM1 D08 0:150 1:150 A:36914350;C:20424845;G:69296209;T:36937661;N:1335 150 150     36914350 20424845 69296209 36937661 1335 ERX14339235 ERS24360053 ERA33112562 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19291 19291 ERR14934860 ERX14339102 ERS24360026 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B05 Humanized Plate 1 Well B05 SAMEA118224949 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B05|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B05|scientific name:Danio rerio                 Raw reads: Sample HUM1 B05 webin reads Sample HUM1 B05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B05.R1.fastq.gz B05.R2.fastq.gz fastq fastq 104906100.0 349687.0 webin reads Sample HUM1 B05 0:150 1:150 A:27195212;C:13543121;G:38418859;T:25748246;N:662 150 150     27195212 13543121 38418859 25748246 662 ERX14339102 ERS24360026 ERA33112153 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19292 19292 ERR14937153 ERX14341397 ERS24422823 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G12 Humanized Plate 2 Well G12 SAMEA118242649 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 G12|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 G12|scientific name:Danio rerio                 Raw reads: Sample HUM2 G12 webin reads Sample HUM2 G12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 G12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G12.R1.fastq.gz G12.R2.fastq.gz fastq fastq 4617277800.0 15390926.0 webin reads Sample HUM2 G12 0:150 1:150 A:1158729179;C:728158561;G:1691881391;T:1038487859;N:20810 150 150     1158729179 728158561 1691881391 1038487859 20810 ERX14341397 ERS24422823 ERA33115725 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19293 19293 ERR14943976 ERX14348128 ERS24422873 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A09 Knockout Plate Well A09 SAMEA118242699 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO A09|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO A09|scientific name:Danio rerio                 Raw reads: Sample KO A09 webin reads Sample KO A09   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO A09 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A09.R1.fastq.gz A09.R2.fastq.gz fastq fastq 7026339600.0 23421132.0 webin reads Sample KO A09 0:150 1:150 A:2584462615;C:932829225;G:1126129540;T:2382863475;N:54745 150 150     2584462615 932829225 1126129540 2382863475 54745 ERX14348128 ERS24422873 ERA33119655 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19294 19294 ERR14934848 ERX14339090 ERS24360022 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B01 Humanized Plate 1 Well B01 SAMEA118224945 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 B01|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 B01|scientific name:Danio rerio                 Raw reads: Sample HUM1 B01 webin reads Sample HUM1 B01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 B01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B01.R1.fastq.gz B01.R2.fastq.gz fastq fastq 75625800.0 252086.0 webin reads Sample HUM1 B01 0:150 1:150 A:11997345;C:9943452;G:40709427;T:12974865;N:711 150 150     11997345 9943452 40709427 12974865 711 ERX14339090 ERS24360022 ERA33112111 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19295 19295 ERR14934832 ERX14339074 ERS24360016 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A07 Humanized Plate 1 Well A07 SAMEA118224939 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A07|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A07|scientific name:Danio rerio                 Raw reads: Sample HUM1 A07 webin reads Sample HUM1 A07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A07.R1.fastq.gz A07.R2.fastq.gz fastq fastq 69187800.0 230626.0 webin reads Sample HUM1 A07 0:150 1:150 A:12381283;C:7906319;G:37465324;T:11434563;N:311 150 150     12381283 7906319 37465324 11434563 311 ERX14339074 ERS24360016 ERA33112056 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19296 19296 ERR14935010 ERX14339252 ERS24360060 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E03 Humanized Plate 1 Well E03 SAMEA118224983 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 E03|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 E03|scientific name:Danio rerio                 Raw reads: Sample HUM1 E03 webin reads Sample HUM1 E03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 E03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E03.R1.fastq.gz E03.R2.fastq.gz fastq fastq 425713200.0 1419044.0 webin reads Sample HUM1 E03 0:150 1:150 A:136345366;C:51139029;G:106693807;T:131531022;N:3976 150 150     136345366 51139029 106693807 131531022 3976 ERX14339252 ERS24360060 ERA33112619 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19297 19297 ERR14937160 ERX14341404 ERS24422830 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H07 Humanized Plate 2 Well H07 SAMEA118242656 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 H07|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 H07|scientific name:Danio rerio                 Raw reads: Sample HUM2 H07 webin reads Sample HUM2 H07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 H07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H07.R1.fastq.gz H07.R2.fastq.gz fastq fastq 2014913100.0 6716377.0 webin reads Sample HUM2 H07 0:150 1:150 A:411170361;C:304335223;G:896421902;T:402976937;N:8677 150 150     411170361 304335223 896421902 402976937 8677 ERX14341404 ERS24422830 ERA33115735 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19298 19298 ERR14936962 ERX14341204 ERS24422793 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E06 Humanized Plate 2 Well E06 SAMEA118242619 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 E06|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 E06|scientific name:Danio rerio                 Raw reads: Sample HUM2 E06 webin reads Sample HUM2 E06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 E06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E06.R1.fastq.gz E06.R2.fastq.gz fastq fastq 10133040000.0 33776800.0 webin reads Sample HUM2 E06 0:150 1:150 A:3260003556;C:1412856784;G:2700597066;T:2759534229;N:48365 150 150     3260003556 1412856784 2700597066 2759534229 48365 ERX14341204 ERS24422793 ERA33115605 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19299 19299 ERR14950764 ERX14354888 ERS24422920 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F05 Knockout Plate Well F05 SAMEA118242746 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO F05|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO F05|scientific name:Danio rerio                 Raw reads: Sample KO F05 webin reads Sample KO F05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO F05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F05.R1.fastq.gz F05.R2.fastq.gz fastq fastq 6748159500.0 22493865.0 webin reads Sample KO F05 0:150 1:150 A:2431257026;C:944096584;G:1125684524;T:2247068351;N:53015 150 150     2431257026 944096584 1125684524 2247068351 53015 ERX14354888 ERS24422920 ERA33121260 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19300 19300 ERR14936821 ERX14341063 ERS24422744 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A05 Humanized Plate 2 Well A05 SAMEA118242570 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 A05|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 A05|scientific name:Danio rerio                 Raw reads: Sample HUM2 A05 webin reads Sample HUM2 A05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 A05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A05.R1.fastq.gz A05.R2.fastq.gz fastq fastq 3531016500.0 11770055.0 webin reads Sample HUM2 A05 0:150 1:150 A:908506275;C:540353948;G:1299418302;T:782721784;N:16191 150 150     908506275 540353948 1299418302 782721784 16191 ERX14341063 ERS24422744 ERA33115508 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19301 19301 ERR14950698 ERX14354822 ERS24422903 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D03 Knockout Plate Well D03 SAMEA118242729 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO D03|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO D03|scientific name:Danio rerio                 Raw reads: Sample KO D03 webin reads Sample KO D03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO D03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D03.R1.fastq.gz D03.R2.fastq.gz fastq fastq 15044100900.0 50147003.0 webin reads Sample KO D03 0:150 1:150 A:5448629271;C:2142046198;G:2372663075;T:5080644849;N:117507 150 150     5448629271 2142046198 2372663075 5080644849 117507 ERX14354822 ERS24422903 ERA33121193 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19302 19302 ERR14950732 ERX14354856 ERS24422910 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well E07 Knockout Plate Well E07 SAMEA118242736 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO E07|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO E07|scientific name:Danio rerio                 Raw reads: Sample KO E07 webin reads Sample KO E07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO E07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 E07.R1.fastq.gz E07.R2.fastq.gz fastq fastq 12898175700.0 42993919.0 webin reads Sample KO E07 0:150 1:150 A:4589735008;C:1839814686;G:2098030544;T:4370493808;N:101654 150 150     4589735008 1839814686 2098030544 4370493808 101654 ERX14354856 ERS24422910 ERA33121227 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19303 19303 ERR14934842 ERX14339084 ERS24360020 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A11 Humanized Plate 1 Well A11 SAMEA118224943 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A11|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A11|scientific name:Danio rerio                 Raw reads: Sample HUM1 A11 webin reads Sample HUM1 A11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A11.R1.fastq.gz A11.R2.fastq.gz fastq fastq 53858400.0 179528.0 webin reads Sample HUM1 A11 0:150 1:150 A:12307549;C:6368678;G:23753869;T:11428030;N:274 150 150     12307549 6368678 23753869 11428030 274 ERX14339084 ERS24360020 ERA33112092 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19304 19304 ERR14950672 ERX14354796 ERS24422899 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C11 Knockout Plate Well C11 SAMEA118242725 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO C11|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO C11|scientific name:Danio rerio                 Raw reads: Sample KO C11 webin reads Sample KO C11   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO C11 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C11.R1.fastq.gz C11.R2.fastq.gz fastq fastq 6484306200.0 21614354.0 webin reads Sample KO C11 0:150 1:150 A:2345044923;C:858634350;G:1122803400;T:2157772266;N:51261 150 150     2345044923 858634350 1122803400 2157772266 51261 ERX14354796 ERS24422899 ERA33121167 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19305 19305 ERR14934989 ERX14339231 ERS24360051 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well D06 Humanized Plate 1 Well D06 SAMEA118224974 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 D06|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 D06|scientific name:Danio rerio                 Raw reads: Sample HUM1 D06 webin reads Sample HUM1 D06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 D06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 D06.R1.fastq.gz D06.R2.fastq.gz fastq fastq 110618100.0 368727.0 webin reads Sample HUM1 D06 0:150 1:150 A:26616860;C:14643839;G:43583750;T:25772923;N:728 150 150     26616860 14643839 43583750 25772923 728 ERX14339231 ERS24360051 ERA33112549 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19306 19306 ERR14950801 ERX14354925 ERS24422933 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G06 Knockout Plate Well G06 SAMEA118242759 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO G06|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO G06|scientific name:Danio rerio                 Raw reads: Sample KO G06 webin reads Sample KO G06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO G06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G06.R1.fastq.gz G06.R2.fastq.gz fastq fastq 1620231000.0 5400770.0 webin reads Sample KO G06 0:150 1:150 A:552572070;C:218631707;G:363017635;T:485997489;N:12099 150 150     552572070 218631707 363017635 485997489 12099 ERX14354925 ERS24422933 ERA33121297 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19307 19307 ERR14936889 ERX14341131 ERS24422756 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B05 Humanized Plate 2 Well B05 SAMEA118242582 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 B05|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 B05|scientific name:Danio rerio                 Raw reads: Sample HUM2 B05 webin reads Sample HUM2 B05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 B05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B05.R1.fastq.gz B05.R2.fastq.gz fastq fastq 9672318000.0 32241060.0 webin reads Sample HUM2 B05 0:150 1:150 A:3355070462;C:1344914308;G:2133672630;T:2838610016;N:50584 150 150     3355070462 1344914308 2133672630 2838610016 50584 ERX14341131 ERS24422756 ERA33115569 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19308 19308 ERR14936826 ERX14341068 ERS24422749 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A10 Humanized Plate 2 Well A10 SAMEA118242575 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 A10|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 A10|scientific name:Danio rerio                 Raw reads: Sample HUM2 A10 webin reads Sample HUM2 A10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 A10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A10.R1.fastq.gz A10.R2.fastq.gz fastq fastq 3319486500.0 11064955.0 webin reads Sample HUM2 A10 0:150 1:150 A:667756780;C:505774653;G:1498623562;T:647316121;N:15384 150 150     667756780 505774653 1498623562 647316121 15384 ERX14341068 ERS24422749 ERA33115516 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19309 19309 ERR14950797 ERX14354921 ERS24422931 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G04 Knockout Plate Well G04 SAMEA118242757 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO G04|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO G04|scientific name:Danio rerio                 Raw reads: Sample KO G04 webin reads Sample KO G04   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO G04 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G04.R1.fastq.gz G04.R2.fastq.gz fastq fastq 1169241600.0 3897472.0 webin reads Sample KO G04 0:150 1:150 A:414405945;C:160380699;G:232288284;T:362157277;N:9395 150 150     414405945 160380699 232288284 362157277 9395 ERX14354921 ERS24422931 ERA33121293 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19310 19310 ERR14935076 ERX14339318 ERS24360081 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F12 Humanized Plate 1 Well F12 SAMEA118225004 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 F12|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 F12|scientific name:Danio rerio                 Raw reads: Sample HUM1 F12 webin reads Sample HUM1 F12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 F12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F12.R1.fastq.gz F12.R2.fastq.gz fastq fastq 460315800.0 1534386.0 webin reads Sample HUM1 F12 0:150 1:150 A:151663513;C:57564329;G:101614217;T:149469927;N:3814 150 150     151663513 57564329 101614217 149469927 3814 ERX14339318 ERS24360081 ERA33112847 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B mate1-mate2 similar by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19311 19311 ERR14950818 ERX14354942 ERS24422939 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G12 Knockout Plate Well G12 SAMEA118242765 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO G12|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO G12|scientific name:Danio rerio                 Raw reads: Sample KO G12 webin reads Sample KO G12   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO G12 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G12.R1.fastq.gz G12.R2.fastq.gz fastq fastq 413542200.0 1378474.0 webin reads Sample KO G12 0:150 1:150 A:126933895;C:59697863;G:113997315;T:112909944;N:3183 150 150     126933895 59697863 113997315 112909944 3183 ERX14354942 ERS24422939 ERA33121314 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19312 19312 ERR14950814 ERX14354938 ERS24422937 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G10 Knockout Plate Well G10 SAMEA118242763 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample KO G10|collection date:2022 05 13|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample KO G10|scientific name:Danio rerio                 Raw reads: Sample KO G10 webin reads Sample KO G10   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample KO G10 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G10.R1.fastq.gz G10.R2.fastq.gz fastq fastq 4954517100.0 16515057.0 webin reads Sample KO G10 0:150 1:150 A:1782759867;C:666395120;G:897330151;T:1607991435;N:40527 150 150     1782759867 666395120 897330151 1607991435 40527 ERX14354938 ERS24422937 ERA33121310 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19313 19313 ERR14937147 ERX14341391 ERS24422817 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well G06 Humanized Plate 2 Well G06 SAMEA118242643 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 G06|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 G06|scientific name:Danio rerio                 Raw reads: Sample HUM2 G06 webin reads Sample HUM2 G06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 G06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 G06.R1.fastq.gz G06.R2.fastq.gz fastq fastq 2593562100.0 8645207.0 webin reads Sample HUM2 G06 0:150 1:150 A:506680806;C:379714116;G:1209306962;T:497848288;N:11928 150 150     506680806 379714116 1209306962 497848288 11928 ERX14341391 ERS24422817 ERA33115717 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19314 19314 ERR14934945 ERX14339187 ERS24360040 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C07 Humanized Plate 1 Well C07 SAMEA118224963 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 C07|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 C07|scientific name:Danio rerio                 Raw reads: Sample HUM1 C07 webin reads Sample HUM1 C07   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 C07 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C07.R1.fastq.gz C07.R2.fastq.gz fastq fastq 790847700.0 2636159.0 webin reads Sample HUM1 C07 0:150 1:150 A:263705480;C:97469638;G:157169342;T:272496337;N:6903 150 150     263705480 97469638 157169342 272496337 6903 ERX14339187 ERS24360040 ERA33112383 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19315 19315 ERR14937112 ERX14341356 ERS24422805 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well F06 Humanized Plate 2 Well F06 SAMEA118242631 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 F06|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 F06|scientific name:Danio rerio                 Raw reads: Sample HUM2 F06 webin reads Sample HUM2 F06   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 F06 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 F06.R1.fastq.gz F06.R2.fastq.gz fastq fastq 3966322200.0 13221074.0 webin reads Sample HUM2 F06 0:150 1:150 A:1063715250;C:596736050;G:1376244952;T:929607538;N:18410 150 150     1063715250 596736050 1376244952 929607538 18410 ERX14341356 ERS24422805 ERA33115694 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19316 19316 ERR14936848 ERX14341090 ERS24422752 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well B01 Humanized Plate 2 Well B01 SAMEA118242578 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 B01|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 B01|scientific name:Danio rerio                 Raw reads: Sample HUM2 B01 webin reads Sample HUM2 B01   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 B01 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 B01.R1.fastq.gz B01.R2.fastq.gz fastq fastq 3646476600.0 12154922.0 webin reads Sample HUM2 B01 0:150 1:150 A:707531998;C:558638966;G:1658431639;T:721858281;N:15716 150 150     707531998 558638966 1658431639 721858281 15716 ERX14341090 ERS24422752 ERA33115539 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19317 19317 ERR14937156 ERX14341400 ERS24422826 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well H03 Humanized Plate 2 Well H03 SAMEA118242652 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 H03|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 H03|scientific name:Danio rerio                 Raw reads: Sample HUM2 H03 webin reads Sample HUM2 H03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 H03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 H03.R1.fastq.gz H03.R2.fastq.gz fastq fastq 4016079900.0 13386933.0 webin reads Sample HUM2 H03 0:150 1:150 A:922587541;C:602672094;G:1679136141;T:811666051;N:18073 150 150     922587541 602672094 1679136141 811666051 18073 ERX14341400 ERS24422826 ERA33115728 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19318 19318 ERR14936909 ERX14341151 ERS24422768 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well C05 Humanized Plate 2 Well C05 SAMEA118242594 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 C05|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 C05|scientific name:Danio rerio                 Raw reads: Sample HUM2 C05 webin reads Sample HUM2 C05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 C05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 C05.R1.fastq.gz C05.R2.fastq.gz fastq fastq 5239985700.0 17466619.0 webin reads Sample HUM2 C05 0:150 1:150 A:1245746806;C:810518138;G:2012815334;T:1170881716;N:23706 150 150     1245746806 810518138 2012815334 1170881716 23706 ERX14341151 ERS24422768 ERA33115592 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19319 19319 ERR14936819 ERX14341061 ERS24422742 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A03 Humanized Plate 2 Well A03 SAMEA118242568 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM2 A03|collection date:2022 12 21|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM2 A03|scientific name:Danio rerio                 Raw reads: Sample HUM2 A03 webin reads Sample HUM2 A03   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM2 A03 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A03.R1.fastq.gz A03.R2.fastq.gz fastq fastq 3879462600.0 12931542.0 webin reads Sample HUM2 A03 0:150 1:150 A:772585320;C:556552679;G:1768725862;T:781581610;N:17129 150 150     772585320 556552679 1768725862 781581610 17129 ERX14341061 ERS24422742 ERA33115506 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System
19320 19320 ERR14934828 ERX14339070 ERS24360014 ERP166068 PRJEB82358 Human gene duplications 53f6d331-4985-4b69-8ac3-a57d010118dd Other Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution. ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23   Single cell RNA sequencing of zebrafish heads from well A05 Humanized Plate 1 Well A05 SAMEA118224937 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2025 05 23|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample HUM1 A05|collection date:2022 11 14|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample HUM1 A05|scientific name:Danio rerio                 Raw reads: Sample HUM1 A05 webin reads Sample HUM1 A05   unspecified   ENA STATUS ID:4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166068 Raw reads: Sample HUM1 A05 ENA STATUS ID:4|ENA FIRST PUBLIC:2025 05 23|ENA LAST UPDATE:2025 05 23 A05.R1.fastq.gz A05.R2.fastq.gz fastq fastq 82488600.0 274962.0 webin reads Sample HUM1 A05 0:150 1:150 A:20156496;C:10667626;G:33017557;T:18646523;N:398 150 150     20156496 10667626 33017557 18646523 398 ERX14339070 ERS24360014 ERA33112037 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                       T T mates < 9% mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-05-23 Larval Larval Head Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;