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
10176,ERR5858457,ERX5504346,ERS6343450,ERP128749,PRJEB44676,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10390,Transcriptome Analysis,To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Naive,SAMEA8658904,University Of Edinburgh,ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10390:Naive p,Naive p,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128749,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,Naive.bam,bam,44972162730.0,499690697.0,E MTAB 10390:Naive,0:90,A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100,90,,,,13658826375,8733304343,9348137569,13228064343,3830100,ERX5504346,ERS6343450,ERA4142789,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.89428,,0.32693,,0.75276,,0.5314,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-05-24,Larval,Larval,Spinal Cord,Nervous System
10186,ERR6212423,ERX5847531,ERS7094943,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Naive,SAMEA9361876,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Naive p,Naive p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz,fastq fastq fastq,60168324125.0,481346593.0,E MTAB 10379 3:Naive,0:8 1:27 2:90,A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241,8,27,90,,12424400694,9366563781,10029312355,11497237299,3679241,ERX5847531,ERS7094943,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.94834,,0.09482,,0.802,,0.5277,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10187,ERR6212422,ERX5847530,ERS7094942,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Lesi1d,SAMEA9361875,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Lesioned p,Lesioned p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:spinal cord lesion,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz,fastq fastq fastq,61701873000.0,493614984.0,E MTAB 10379 3:Lesioned,0:8 1:27 2:90,A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277,8,27,90,,12952533019,9222397450,9920185920,12326470894,3761277,ERX5847530,ERS7094942,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.93082,,0.10862,,0.80302,,0.54924,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
11134,ERR9981089,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz,fastq fastq,60177283876.0,509976982.0,E MTAB 11991:P25452 2002 S2 L001,0:28 1:90,A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481,28,90,,,17254566438,13547211711,14188233429,15185192817,2079481,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00671,0.93031,0.00231,0.11028,0.9932,0.82227,0.30887,0.58272,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11135,ERR9981090,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz,fastq fastq,60597886144.0,513541408.0,E MTAB 11991:P25452 2002 S2 L002,0:28 1:90,A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626,28,90,,,17368154358,13649089056,14296037620,15282869484,1735626,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00656,0.92899,0.00211,0.11059,0.99334,0.82335,0.32311,0.57644,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11136,ERR9981087,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz,fastq fastq,20866120186.0,176831527.0,E MTAB 11991:P25452 2001 S1 L001,0:28 1:90,A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046,28,90,,,5933525376,4737179804,5025711080,5168983880,720046,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00805,0.92622,0.00259,0.11842,0.99302,0.83027,0.2729,0.57699,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11137,ERR9981088,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz,fastq fastq,21068682172.0,178548154.0,E MTAB 11991:P25452 2001 S1 L002,0:28 1:90,A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528,28,90,,,5987758267,4786100132,5078292970,5215926275,604528,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00813,0.92702,0.00264,0.11874,0.99283,0.82737,0.30228,0.56929,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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