metadata: run_metadata: 1,550 rows where devstage_curation = "Larval" and experiment.library

1,550 rows where devstage_curation = "Larval" and experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10176	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	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	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	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 u…	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 w…	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	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 u…	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 w…	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	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 u…	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 w…	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	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 u…	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 w…	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	19221	ERR14935135	ERX14339377	ERS24360099	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H06	Humanized Plate 1 Well H06	SAMEA118225022	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H06\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H06\|scientific name:Danio rerio	Raw reads: Sample HUM1 H06	webin reads Sample HUM1 H06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H06.R1.fastq.gz H06.R2.fastq.gz	fastq fastq	168135000.0	560450.0	webin reads Sample HUM1 H06	0:150 1:150	A:49336993;C:19637394;G:50002867;T:49156187;N:1559	150	150		49336993	19637394	50002867	49156187	1559	ERX14339377	ERS24360099	ERA33113052	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19222	19222	ERR14934924	ERX14339166	ERS24360038	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C05	Humanized Plate 1 Well C05	SAMEA118224961	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 C05\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 C05\|scientific name:Danio rerio	Raw reads: Sample HUM1 C05	webin reads Sample HUM1 C05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 C05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C05.R1.fastq.gz C05.R2.fastq.gz	fastq fastq	406863000.0	1356210.0	webin reads Sample HUM1 C05	0:150 1:150	A:135043675;C:48707343;G:87607964;T:135501103;N:2915	150	150		135043675	48707343	87607964	135501103	2915	ERX14339166	ERS24360038	ERA33112290	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19223	19223	ERR14934974	ERX14339216	ERS24360047	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D02	Humanized Plate 1 Well D02	SAMEA118224970	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 D02\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 D02\|scientific name:Danio rerio	Raw reads: Sample HUM1 D02	webin reads Sample HUM1 D02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 D02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D02.R1.fastq.gz D02.R2.fastq.gz	fastq fastq	231350700.0	771169.0	webin reads Sample HUM1 D02	0:150 1:150	A:61554211;C:27195025;G:82686912;T:59912853;N:1699	150	150		61554211	27195025	82686912	59912853	1699	ERX14339216	ERS24360047	ERA33112492	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19224	19224	ERR14937148	ERX14341392	ERS24422818	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G07	Humanized Plate 2 Well G07	SAMEA118242644	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 G07\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 G07\|scientific name:Danio rerio	Raw reads: Sample HUM2 G07	webin reads Sample HUM2 G07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 G07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G07.R1.fastq.gz G07.R2.fastq.gz	fastq fastq	1858827300.0	6196091.0	webin reads Sample HUM2 G07	0:150 1:150	A:377243729;C:275647713;G:834077378;T:371849924;N:8556	150	150		377243729	275647713	834077378	371849924	8556	ERX14341392	ERS24422818	ERA33115718	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19225	19225	ERR14935143	ERX14339385	ERS24360101	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H08	Humanized Plate 1 Well H08	SAMEA118225024	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H08\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H08\|scientific name:Danio rerio	Raw reads: Sample HUM1 H08	webin reads Sample HUM1 H08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H08.R1.fastq.gz H08.R2.fastq.gz	fastq fastq	104513100.0	348377.0	webin reads Sample HUM1 H08	0:150 1:150	A:24551652;C:12552824;G:43587381;T:23820238;N:1005	150	150		24551652	12552824	43587381	23820238	1005	ERX14339385	ERS24360101	ERA33113082	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19226	19226	ERR14936904	ERX14341146	ERS24422763	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B12	Humanized Plate 2 Well B12	SAMEA118242589	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 B12\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 B12\|scientific name:Danio rerio	Raw reads: Sample HUM2 B12	webin reads Sample HUM2 B12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 B12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B12.R1.fastq.gz B12.R2.fastq.gz	fastq fastq	14783024100.0	49276747.0	webin reads Sample HUM2 B12	0:150 1:150	A:4993941125;C:1900193626;G:3694935207;T:4193880937;N:73205	150	150		4993941125	1900193626	3694935207	4193880937	73205	ERX14341146	ERS24422763	ERA33115587	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19227	19227	ERR14935120	ERX14339362	ERS24360094	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H01	Humanized Plate 1 Well H01	SAMEA118225017	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H01\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H01\|scientific name:Danio rerio	Raw reads: Sample HUM1 H01	webin reads Sample HUM1 H01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H01.R1.fastq.gz H01.R2.fastq.gz	fastq fastq	214281900.0	714273.0	webin reads Sample HUM1 H01	0:150 1:150	A:63612930;C:24945238;G:64455038;T:61267490;N:1204	150	150		63612930	24945238	64455038	61267490	1204	ERX14339362	ERS24360094	ERA33112989	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19228	19228	ERR14935021	ERX14339263	ERS24360064	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E07	Humanized Plate 1 Well E07	SAMEA118224987	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 E07\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 E07\|scientific name:Danio rerio	Raw reads: Sample HUM1 E07	webin reads Sample HUM1 E07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 E07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E07.R1.fastq.gz E07.R2.fastq.gz	fastq fastq	274863600.0	916212.0	webin reads Sample HUM1 E07	0:150 1:150	A:89634361;C:31803602;G:65721376;T:87702420;N:1841	150	150		89634361	31803602	65721376	87702420	1841	ERX14339263	ERS24360064	ERA33112659	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19229	19229	ERR14950666	ERX14354790	ERS24422897	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C09	Knockout Plate Well C09	SAMEA118242723	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO C09\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO C09\|scientific name:Danio rerio	Raw reads: Sample KO C09	webin reads Sample KO C09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO C09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C09.R1.fastq.gz C09.R2.fastq.gz	fastq fastq	12910892700.0	43036309.0	webin reads Sample KO C09	0:150 1:150	A:4656205100;C:1791783755;G:2065221420;T:4397579948;N:102477	150	150		4656205100	1791783755	2065221420	4397579948	102477	ERX14354790	ERS24422897	ERA33121161	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19230	19230	ERR14936878	ERX14341120	ERS24422755	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B04	Humanized Plate 2 Well B04	SAMEA118242581	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 B04\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 B04\|scientific name:Danio rerio	Raw reads: Sample HUM2 B04	webin reads Sample HUM2 B04		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 B04	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B04.R1.fastq.gz B04.R2.fastq.gz	fastq fastq	2614344300.0	8714481.0	webin reads Sample HUM2 B04	0:150 1:150	A:495532634;C:388504084;G:1222436337;T:507858943;N:12302	150	150		495532634	388504084	1222436337	507858943	12302	ERX14341120	ERS24422755	ERA33115558	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19231	19231	ERR14950561	ERX14354685	ERS24422871	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A07	Knockout Plate Well A07	SAMEA118242697	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO A07\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO A07\|scientific name:Danio rerio	Raw reads: Sample KO A07	webin reads Sample KO A07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO A07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A07.R1.fastq.gz A07.R2.fastq.gz	fastq fastq	3401128800.0	11337096.0	webin reads Sample KO A07	0:150 1:150	A:1234869505;C:459023584;G:579824655;T:1127383390;N:27666	150	150		1234869505	459023584	579824655	1127383390	27666	ERX14354685	ERS24422871	ERA33121056	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19232	19232	ERR14936823	ERX14341065	ERS24422746	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A07	Humanized Plate 2 Well A07	SAMEA118242572	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 A07\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 A07\|scientific name:Danio rerio	Raw reads: Sample HUM2 A07	webin reads Sample HUM2 A07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 A07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A07.R1.fastq.gz A07.R2.fastq.gz	fastq fastq	3778502100.0	12595007.0	webin reads Sample HUM2 A07	0:150 1:150	A:710336891;C:494217522;G:1880968771;T:692961837;N:17079	150	150		710336891	494217522	1880968771	692961837	17079	ERX14341065	ERS24422746	ERA33115511	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19233	19233	ERR14937143	ERX14341387	ERS24422813	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G02	Humanized Plate 2 Well G02	SAMEA118242639	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 G02\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 G02\|scientific name:Danio rerio	Raw reads: Sample HUM2 G02	webin reads Sample HUM2 G02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 G02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G02.R1.fastq.gz G02.R2.fastq.gz	fastq fastq	5962135800.0	19873786.0	webin reads Sample HUM2 G02	0:150 1:150	A:1745436521;C:821720129;G:1863789129;T:1531162608;N:27413	150	150		1745436521	821720129	1863789129	1531162608	27413	ERX14341387	ERS24422813	ERA33115710	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19234	19234	ERR14934810	ERX14339052	ERS24360011	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A02	Humanized Plate 1 Well A02	SAMEA118224934	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 A02\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 A02\|scientific name:Danio rerio	Raw reads: Sample HUM1 A02	webin reads Sample HUM1 A02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 A02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A02.R1.fastq.gz A02.R2.fastq.gz	fastq fastq	480559200.0	1601864.0	webin reads Sample HUM1 A02	0:150 1:150	A:163177108;C:53718756;G:98835089;T:164825485;N:2762	150	150		163177108	53718756	98835089	164825485	2762	ERX14339052	ERS24360011	ERA33111955	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19235	19235	ERR14934984	ERX14339226	ERS24360049	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D04	Humanized Plate 1 Well D04	SAMEA118224972	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 D04\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 D04\|scientific name:Danio rerio	Raw reads: Sample HUM1 D04	webin reads Sample HUM1 D04		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 D04	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D04.R1.fastq.gz D04.R2.fastq.gz	fastq fastq	179225700.0	597419.0	webin reads Sample HUM1 D04	0:150 1:150	A:45457519;C:22876690;G:67395901;T:43493765;N:1825	150	150		45457519	22876690	67395901	43493765	1825	ERX14339226	ERS24360049	ERA33112537	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19236	19236	ERR14934845	ERX14339087	ERS24360021	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A12	Humanized Plate 1 Well A12	SAMEA118224944	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 A12\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 A12\|scientific name:Danio rerio	Raw reads: Sample HUM1 A12	webin reads Sample HUM1 A12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 A12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A12.R1.fastq.gz A12.R2.fastq.gz	fastq fastq	77425200.0	258084.0	webin reads Sample HUM1 A12	0:150 1:150	A:16644810;C:10391814;G:34720928;T:15667259;N:389	150	150		16644810	10391814	34720928	15667259	389	ERX14339087	ERS24360021	ERA33112104	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19237	19237	ERR14934855	ERX14339097	ERS24360024	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B03	Humanized Plate 1 Well B03	SAMEA118224947	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B03\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B03\|scientific name:Danio rerio	Raw reads: Sample HUM1 B03	webin reads Sample HUM1 B03		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B03	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B03.R1.fastq.gz B03.R2.fastq.gz	fastq fastq	94155000.0	313850.0	webin reads Sample HUM1 B03	0:150 1:150	A:23101292;C:11479599;G:38484223;T:21089074;N:812	150	150		23101292	11479599	38484223	21089074	812	ERX14339097	ERS24360024	ERA33112137	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19238	19238	ERR14943975	ERX14348127	ERS24422869	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A05	Knockout Plate Well A05	SAMEA118242695	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO A05\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO A05\|scientific name:Danio rerio	Raw reads: Sample KO A05	webin reads Sample KO A05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO A05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A05.R1.fastq.gz A05.R2.fastq.gz	fastq fastq	3911878200.0	13039594.0	webin reads Sample KO A05	0:150 1:150	A:1402938003;C:529582691;G:715316068;T:1264010327;N:31111	150	150		1402938003	529582691	715316068	1264010327	31111	ERX14348127	ERS24422869	ERA33119600	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19239	19239	ERR14937117	ERX14341361	ERS24422810	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F11	Humanized Plate 2 Well F11	SAMEA118242636	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 F11\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 F11\|scientific name:Danio rerio	Raw reads: Sample HUM2 F11	webin reads Sample HUM2 F11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 F11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F11.R1.fastq.gz F11.R2.fastq.gz	fastq fastq	3943764300.0	13145881.0	webin reads Sample HUM2 F11	0:150 1:150	A:1194917338;C:577472498;G:1192413538;T:978942667;N:18259	150	150		1194917338	577472498	1192413538	978942667	18259	ERX14341361	ERS24422810	ERA33115700	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19240	19240	ERR14935149	ERX14339391	ERS24360104	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H11	Humanized Plate 1 Well H11	SAMEA118225027	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H11\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H11\|scientific name:Danio rerio	Raw reads: Sample HUM1 H11	webin reads Sample HUM1 H11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H11.R1.fastq.gz H11.R2.fastq.gz	fastq fastq	29087400.0	96958.0	webin reads Sample HUM1 H11	0:150 1:150	A:5335277;C:3932942;G:14621885;T:5197119;N:177	150	150		5335277	3932942	14621885	5197119	177	ERX14339391	ERS24360104	ERA33113103	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19241	19241	ERR14935025	ERX14339267	ERS24360065	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E08	Humanized Plate 1 Well E08	SAMEA118224988	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 E08\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 E08\|scientific name:Danio rerio	Raw reads: Sample HUM1 E08	webin reads Sample HUM1 E08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 E08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E08.R1.fastq.gz E08.R2.fastq.gz	fastq fastq	220002300.0	733341.0	webin reads Sample HUM1 E08	0:150 1:150	A:62013327;C:25647839;G:72394925;T:59944865;N:1344	150	150		62013327	25647839	72394925	59944865	1344	ERX14339267	ERS24360065	ERA33112670	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19242	19242	ERR14935108	ERX14339350	ERS24360090	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G09	Humanized Plate 1 Well G09	SAMEA118225013	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 G09\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 G09\|scientific name:Danio rerio	Raw reads: Sample HUM1 G09	webin reads Sample HUM1 G09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 G09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G09.R1.fastq.gz G09.R2.fastq.gz	fastq fastq	55286400.0	184288.0	webin reads Sample HUM1 G09	0:150 1:150	A:9253015;C:6978214;G:29393822;T:9661042;N:307	150	150		9253015	6978214	29393822	9661042	307	ERX14339350	ERS24360090	ERA33112953	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19243	19243	ERR14935106	ERX14339348	ERS24360089	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G08	Humanized Plate 1 Well G08	SAMEA118225012	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 G08\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 G08\|scientific name:Danio rerio	Raw reads: Sample HUM1 G08	webin reads Sample HUM1 G08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 G08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G08.R1.fastq.gz G08.R2.fastq.gz	fastq fastq	90390000.0	301300.0	webin reads Sample HUM1 G08	0:150 1:150	A:14519869;C:11004100;G:49374862;T:15490478;N:691	150	150		14519869	11004100	49374862	15490478	691	ERX14339348	ERS24360089	ERA33112948	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19244	19244	ERR14934877	ERX14339119	ERS24360032	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B11	Humanized Plate 1 Well B11	SAMEA118224955	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B11\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B11\|scientific name:Danio rerio	Raw reads: Sample HUM1 B11	webin reads Sample HUM1 B11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B11.R1.fastq.gz B11.R2.fastq.gz	fastq fastq	99908700.0	333029.0	webin reads Sample HUM1 B11	0:150 1:150	A:22260827;C:11949991;G:42744522;T:22952623;N:737	150	150		22260827	11949991	42744522	22952623	737	ERX14339119	ERS24360032	ERA33112207	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19245	19245	ERR14934885	ERX14339127	ERS24360034	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C01	Humanized Plate 1 Well C01	SAMEA118224957	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 C01\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 C01\|scientific name:Danio rerio	Raw reads: Sample HUM1 C01	webin reads Sample HUM1 C01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 C01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C01.R1.fastq.gz C01.R2.fastq.gz	fastq fastq	101124300.0	337081.0	webin reads Sample HUM1 C01	0:150 1:150	A:21597244;C:13549354;G:45547786;T:20429406;N:510	150	150		21597244	13549354	45547786	20429406	510	ERX14339127	ERS24360034	ERA33112235	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19246	19246	ERR14943984	ERX14348136	ERS24422880	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B04	Knockout Plate Well B04	SAMEA118242706	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO B04\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO B04\|scientific name:Danio rerio	Raw reads: Sample KO B04	webin reads Sample KO B04		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO B04	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B04.R1.fastq.gz B04.R2.fastq.gz	fastq fastq	561237900.0	1870793.0	webin reads Sample KO B04	0:150 1:150	A:192169170;C:77013107;G:120338699;T:171712356;N:4568	150	150		192169170	77013107	120338699	171712356	4568	ERX14348136	ERS24422880	ERA33119691	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19247	19247	ERR14938992	ERX14343236	ERS24422834	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H11	Humanized Plate 2 Well H11	SAMEA118242660	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 H11\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 H11\|scientific name:Danio rerio	Raw reads: Sample HUM2 H11	webin reads Sample HUM2 H11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 H11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H11.R1.fastq.gz H11.R2.fastq.gz	fastq fastq	1733814900.0	5779383.0	webin reads Sample HUM2 H11	0:150 1:150	A:378393702;C:284557462;G:721428373;T:349427441;N:7922	150	150		378393702	284557462	721428373	349427441	7922	ERX14343236	ERS24422834	ERA33115755	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19248	19248	ERR14937159	ERX14341403	ERS24422829	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H06	Humanized Plate 2 Well H06	SAMEA118242655	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 H06\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 H06\|scientific name:Danio rerio	Raw reads: Sample HUM2 H06	webin reads Sample HUM2 H06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 H06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H06.R1.fastq.gz H06.R2.fastq.gz	fastq fastq	8840167200.0	29467224.0	webin reads Sample HUM2 H06	0:150 1:150	A:3070163952;C:1202397032;G:1876790493;T:2690771671;N:44052	150	150		3070163952	1202397032	1876790493	2690771671	44052	ERX14341403	ERS24422829	ERA33115733	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19249	19249	ERR14934852	ERX14339094	ERS24360023	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B02	Humanized Plate 1 Well B02	SAMEA118224946	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B02\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B02\|scientific name:Danio rerio	Raw reads: Sample HUM1 B02	webin reads Sample HUM1 B02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B02.R1.fastq.gz B02.R2.fastq.gz	fastq fastq	123106800.0	410356.0	webin reads Sample HUM1 B02	0:150 1:150	A:24870369;C:15859782;G:60046944;T:22329104;N:601	150	150		24870369	15859782	60046944	22329104	601	ERX14339094	ERS24360023	ERA33112126	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19250	19250	ERR14936902	ERX14341144	ERS24422761	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B10	Humanized Plate 2 Well B10	SAMEA118242587	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 B10\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 B10\|scientific name:Danio rerio	Raw reads: Sample HUM2 B10	webin reads Sample HUM2 B10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 B10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B10.R1.fastq.gz B10.R2.fastq.gz	fastq fastq	3818756100.0	12729187.0	webin reads Sample HUM2 B10	0:150 1:150	A:801009311;C:582803669;G:1691856038;T:743070146;N:16936	150	150		801009311	582803669	1691856038	743070146	16936	ERX14341144	ERS24422761	ERA33115582	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19251	19251	ERR14935145	ERX14339387	ERS24360102	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H09	Humanized Plate 1 Well H09	SAMEA118225025	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H09\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H09\|scientific name:Danio rerio	Raw reads: Sample HUM1 H09	webin reads Sample HUM1 H09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H09.R1.fastq.gz H09.R2.fastq.gz	fastq fastq	79435500.0	264785.0	webin reads Sample HUM1 H09	0:150 1:150	A:19325284;C:9616771;G:32084598;T:18408162;N:685	150	150		19325284	9616771	32084598	18408162	685	ERX14339387	ERS24360102	ERA33113089	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19252	19252	ERR14935006	ERX14339248	ERS24360059	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E02	Humanized Plate 1 Well E02	SAMEA118224982	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 E02\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 E02\|scientific name:Danio rerio	Raw reads: Sample HUM1 E02	webin reads Sample HUM1 E02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 E02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E02.R1.fastq.gz E02.R2.fastq.gz	fastq fastq	184473600.0	614912.0	webin reads Sample HUM1 E02	0:150 1:150	A:47275758;C:21941025;G:68635035;T:46620684;N:1098	150	150		47275758	21941025	68635035	46620684	1098	ERX14339248	ERS24360059	ERA33112606	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19253	19253	ERR14937114	ERX14341358	ERS24422807	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F08	Humanized Plate 2 Well F08	SAMEA118242633	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 F08\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 F08\|scientific name:Danio rerio	Raw reads: Sample HUM2 F08	webin reads Sample HUM2 F08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 F08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F08.R1.fastq.gz F08.R2.fastq.gz	fastq fastq	5604971400.0	18683238.0	webin reads Sample HUM2 F08	0:150 1:150	A:1272096391;C:927796029;G:2253030240;T:1152025287;N:23453	150	150		1272096391	927796029	2253030240	1152025287	23453	ERX14341358	ERS24422807	ERA33115697	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19254	19254	ERR14935115	ERX14339357	ERS24360092	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G11	Humanized Plate 1 Well G11	SAMEA118225015	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 G11\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 G11\|scientific name:Danio rerio	Raw reads: Sample HUM1 G11	webin reads Sample HUM1 G11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 G11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G11.R1.fastq.gz G11.R2.fastq.gz	fastq fastq	18225600.0	60752.0	webin reads Sample HUM1 G11	0:150 1:150	A:3396385;C:2248165;G:9171340;T:3409593;N:117	150	150		3396385	2248165	9171340	3409593	117	ERX14339357	ERS24360092	ERA33112973	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19255	19255	ERR14950748	ERX14354872	ERS24422916	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F01	Knockout Plate Well F01	SAMEA118242742	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO F01\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO F01\|scientific name:Danio rerio	Raw reads: Sample KO F01	webin reads Sample KO F01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO F01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F01.R1.fastq.gz F01.R2.fastq.gz	fastq fastq	3161931900.0	10539773.0	webin reads Sample KO F01	0:150 1:150	A:1111325789;C:460593692;G:495389420;T:1094598021;N:24978	150	150		1111325789	460593692	495389420	1094598021	24978	ERX14354872	ERS24422916	ERA33121243	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19256	19256	ERR14934881	ERX14339123	ERS24360033	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B12	Humanized Plate 1 Well B12	SAMEA118224956	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B12\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B12\|scientific name:Danio rerio	Raw reads: Sample HUM1 B12	webin reads Sample HUM1 B12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B12.R1.fastq.gz B12.R2.fastq.gz	fastq fastq	116537700.0	388459.0	webin reads Sample HUM1 B12	0:150 1:150	A:27658956;C:13844738;G:48483886;T:26549255;N:865	150	150		27658956	13844738	48483886	26549255	865	ERX14339123	ERS24360033	ERA33112224	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19257	19257	ERR14934824	ERX14339066	ERS24360013	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A04	Humanized Plate 1 Well A04	SAMEA118224936	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 A04\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 A04\|scientific name:Danio rerio	Raw reads: Sample HUM1 A04	webin reads Sample HUM1 A04		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 A04	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A04.R1.fastq.gz A04.R2.fastq.gz	fastq fastq	190861200.0	636204.0	webin reads Sample HUM1 A04	0:150 1:150	A:51866429;C:22469460;G:65825429;T:50698008;N:1874	150	150		51866429	22469460	65825429	50698008	1874	ERX14339066	ERS24360013	ERA33112023	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19258	19258	ERR14934950	ERX14339192	ERS24360041	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C08	Humanized Plate 1 Well C08	SAMEA118224964	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 C08\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 C08\|scientific name:Danio rerio	Raw reads: Sample HUM1 C08	webin reads Sample HUM1 C08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 C08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C08.R1.fastq.gz C08.R2.fastq.gz	fastq fastq	347655600.0	1158852.0	webin reads Sample HUM1 C08	0:150 1:150	A:111273717;C:41410769;G:81188146;T:113779846;N:3122	150	150		111273717	41410769	81188146	113779846	3122	ERX14339192	ERS24360041	ERA33112408	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19259	19259	ERR14936959	ERX14341201	ERS24422772	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C09	Humanized Plate 2 Well C09	SAMEA118242598	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 C09\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 C09\|scientific name:Danio rerio	Raw reads: Sample HUM2 C09	webin reads Sample HUM2 C09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 C09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C09.R1.fastq.gz C09.R2.fastq.gz	fastq fastq	3716150400.0	12387168.0	webin reads Sample HUM2 C09	0:150 1:150	A:950093356;C:589554852;G:1341746189;T:834739539;N:16464	150	150		950093356	589554852	1341746189	834739539	16464	ERX14341201	ERS24422772	ERA33115600	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19260	19260	ERR14934954	ERX14339196	ERS24360042	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C09	Humanized Plate 1 Well C09	SAMEA118224965	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 C09\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 C09\|scientific name:Danio rerio	Raw reads: Sample HUM1 C09	webin reads Sample HUM1 C09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 C09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C09.R1.fastq.gz C09.R2.fastq.gz	fastq fastq	160752900.0	535843.0	webin reads Sample HUM1 C09	0:150 1:150	A:47408978;C:19223052;G:47019288;T:47100126;N:1456	150	150		47408978	19223052	47019288	47100126	1456	ERX14339196	ERS24360042	ERA33112423	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19261	19261	ERR14950615	ERX14354739	ERS24422889	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C01	Knockout Plate Well C01	SAMEA118242715	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO C01\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO C01\|scientific name:Danio rerio	Raw reads: Sample KO C01	webin reads Sample KO C01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO C01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C01.R1.fastq.gz C01.R2.fastq.gz	fastq fastq	12926966100.0	43089887.0	webin reads Sample KO C01	0:150 1:150	A:4670066457;C:1792574588;G:2068594468;T:4395628669;N:101918	150	150		4670066457	1792574588	2068594468	4395628669	101918	ERX14354739	ERS24422889	ERA33121110	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19262	19262	ERR14950602	ERX14354726	ERS24422887	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B11	Knockout Plate Well B11	SAMEA118242713	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO B11\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO B11\|scientific name:Danio rerio	Raw reads: Sample KO B11	webin reads Sample KO B11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO B11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B11.R1.fastq.gz B11.R2.fastq.gz	fastq fastq	7240824000.0	24136080.0	webin reads Sample KO B11	0:150 1:150	A:2670219676;C:931192972;G:1216106261;T:2423246169;N:58922	150	150		2670219676	931192972	1216106261	2423246169	58922	ERX14354726	ERS24422887	ERA33121097	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19263	19263	ERR14950677	ERX14354801	ERS24422900	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C12	Knockout Plate Well C12	SAMEA118242726	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO C12\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO C12\|scientific name:Danio rerio	Raw reads: Sample KO C12	webin reads Sample KO C12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO C12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C12.R1.fastq.gz C12.R2.fastq.gz	fastq fastq	8490801000.0	28302670.0	webin reads Sample KO C12	0:150 1:150	A:3049316720;C:1192674579;G:1458160432;T:2790581120;N:68149	150	150		3049316720	1192674579	1458160432	2790581120	68149	ERX14354801	ERS24422900	ERA33121172	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19264	19264	ERR14950597	ERX14354721	ERS24422886	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B10	Knockout Plate Well B10	SAMEA118242712	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO B10\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO B10\|scientific name:Danio rerio	Raw reads: Sample KO B10	webin reads Sample KO B10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO B10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B10.R1.fastq.gz B10.R2.fastq.gz	fastq fastq	9344290800.0	31147636.0	webin reads Sample KO B10	0:150 1:150	A:3401103081;C:1284404735;G:1572646132;T:3086062190;N:74662	150	150		3401103081	1284404735	1572646132	3086062190	74662	ERX14354721	ERS24422886	ERA33121092	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19265	19265	ERR14950734	ERX14354858	ERS24422911	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E08	Knockout Plate Well E08	SAMEA118242737	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO E08\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO E08\|scientific name:Danio rerio	Raw reads: Sample KO E08	webin reads Sample KO E08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO E08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E08.R1.fastq.gz E08.R2.fastq.gz	fastq fastq	1843996200.0	6146654.0	webin reads Sample KO E08	0:150 1:150	A:639221474;C:243164058;G:390761341;T:570834581;N:14746	150	150		639221474	243164058	390761341	570834581	14746	ERX14354858	ERS24422911	ERA33121229	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19266	19266	ERR14943982	ERX14348134	ERS24422877	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B01	Knockout Plate Well B01	SAMEA118242703	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO B01\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO B01\|scientific name:Danio rerio	Raw reads: Sample KO B01	webin reads Sample KO B01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO B01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B01.R1.fastq.gz B01.R2.fastq.gz	fastq fastq	11318469900.0	37728233.0	webin reads Sample KO B01	0:150 1:150	A:4086308197;C:1546883485;G:1844189302;T:3841000200;N:88716	150	150		4086308197	1546883485	1844189302	3841000200	88716	ERX14348134	ERS24422877	ERA33119688	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19267	19267	ERR14950636	ERX14354760	ERS24422893	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C05	Knockout Plate Well C05	SAMEA118242719	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO C05\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO C05\|scientific name:Danio rerio	Raw reads: Sample KO C05	webin reads Sample KO C05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO C05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C05.R2.fastq.gz C05.R1.fastq.gz	fastq fastq	13861467300.0	46204891.0	webin reads Sample KO C05	0:150 1:150	A:4748497970;C:2174952613;G:2309004592;T:4628898110;N:114015	150	150		4748497970	2174952613	2309004592	4628898110	114015	ERX14354760	ERS24422893	ERA33121131	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19268	19268	ERR14935064	ERX14339306	ERS24360078	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F09	Humanized Plate 1 Well F09	SAMEA118225001	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 F09\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 F09\|scientific name:Danio rerio	Raw reads: Sample HUM1 F09	webin reads Sample HUM1 F09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 F09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F09.R1.fastq.gz F09.R2.fastq.gz	fastq fastq	393873600.0	1312912.0	webin reads Sample HUM1 F09	0:150 1:150	A:125159366;C:49326024;G:94522011;T:124863337;N:2862	150	150		125159366	49326024	94522011	124863337	2862	ERX14339306	ERS24360078	ERA33112801	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19269	19269	ERR14934858	ERX14339100	ERS24360025	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B04	Humanized Plate 1 Well B04	SAMEA118224948	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B04\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B04\|scientific name:Danio rerio	Raw reads: Sample HUM1 B04	webin reads Sample HUM1 B04		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B04	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B04.R1.fastq.gz B04.R2.fastq.gz	fastq fastq	85698600.0	285662.0	webin reads Sample HUM1 B04	0:150 1:150	A:16127871;C:10936313;G:42563818;T:16070081;N:517	150	150		16127871	10936313	42563818	16070081	517	ERX14339100	ERS24360025	ERA33112146	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19270	19270	ERR14950548	ERX14354672	ERS24422866	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A02	Knockout Plate Well A02	SAMEA118242692	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO A02\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO A02\|scientific name:Danio rerio	Raw reads: Sample KO A02	webin reads Sample KO A02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO A02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A02.R1.fastq.gz A02.R2.fastq.gz	fastq fastq	3357020700.0	11190069.0	webin reads Sample KO A02	0:150 1:150	A:1198525901;C:478732184;G:572930834;T:1106804630;N:27151	150	150		1198525901	478732184	572930834	1106804630	27151	ERX14354672	ERS24422866	ERA33121043	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19271	19271	ERR14936843	ERX14341085	ERS24422751	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A12	Humanized Plate 2 Well A12	SAMEA118242577	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 A12\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 A12\|scientific name:Danio rerio	Raw reads: Sample HUM2 A12	webin reads Sample HUM2 A12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 A12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A12.R1.fastq.gz A12.R2.fastq.gz	fastq fastq	10256706300.0	34189021.0	webin reads Sample HUM2 A12	0:150 1:150	A:3536584478;C:1403340948;G:2397966213;T:2918763136;N:51525	150	150		3536584478	1403340948	2397966213	2918763136	51525	ERX14341085	ERS24422751	ERA33115534	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19272	19272	ERR14950795	ERX14354919	ERS24422930	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G03	Knockout Plate Well G03	SAMEA118242756	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO G03\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO G03\|scientific name:Danio rerio	Raw reads: Sample KO G03	webin reads Sample KO G03		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO G03	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G03.R1.fastq.gz G03.R2.fastq.gz	fastq fastq	7364946000.0	24549820.0	webin reads Sample KO G03	0:150 1:150	A:2672614853;C:1036322394;G:1247472746;T:2408476880;N:59127	150	150		2672614853	1036322394	1247472746	2408476880	59127	ERX14354919	ERS24422930	ERA33121291	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19273	19273	ERR14935029	ERX14339271	ERS24360067	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E10	Humanized Plate 1 Well E10	SAMEA118224990	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 E10\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 E10\|scientific name:Danio rerio	Raw reads: Sample HUM1 E10	webin reads Sample HUM1 E10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 E10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E10.R1.fastq.gz E10.R2.fastq.gz	fastq fastq	137180100.0	457267.0	webin reads Sample HUM1 E10	0:150 1:150	A:33764068;C:16452119;G:53129173;T:33833524;N:1216	150	150		33764068	16452119	53129173	33833524	1216	ERX14339271	ERS24360067	ERA33112682	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19274	19274	ERR14937113	ERX14341357	ERS24422806	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F07	Humanized Plate 2 Well F07	SAMEA118242632	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 F07\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 F07\|scientific name:Danio rerio	Raw reads: Sample HUM2 F07	webin reads Sample HUM2 F07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 F07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F07.R1.fastq.gz F07.R2.fastq.gz	fastq fastq	3764933100.0	12549777.0	webin reads Sample HUM2 F07	0:150 1:150	A:931279746;C:549119528;G:1391605324;T:892911306;N:17196	150	150		931279746	549119528	1391605324	892911306	17196	ERX14341357	ERS24422806	ERA33115695	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19275	19275	ERR14952973	ERX14357127	ERS24422835	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H12	Humanized Plate 2 Well H12	SAMEA118242661	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 H12\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 H12\|scientific name:Danio rerio	Raw reads: Sample HUM2 H12	webin reads Sample HUM2 H12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 H12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H12.R1.fastq.gz H12.R2.fastq.gz	fastq fastq	4110320400.0	13701068.0	webin reads Sample HUM2 H12	0:150 1:150	A:994038023;C:659909232;G:1578428805;T:877925810;N:18530	150	150		994038023	659909232	1578428805	877925810	18530	ERX14357127	ERS24422835	ERA33122913	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19276	19276	ERR14935019	ERX14339261	ERS24360063	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E06	Humanized Plate 1 Well E06	SAMEA118224986	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 E06\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 E06\|scientific name:Danio rerio	Raw reads: Sample HUM1 E06	webin reads Sample HUM1 E06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 E06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E06.R1.fastq.gz E06.R2.fastq.gz	fastq fastq	250613700.0	835379.0	webin reads Sample HUM1 E06	0:150 1:150	A:75679048;C:30156356;G:70614639;T:74161729;N:1928	150	150		75679048	30156356	70614639	74161729	1928	ERX14339261	ERS24360063	ERA33112650	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19277	19277	ERR14937144	ERX14341388	ERS24422814	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G03	Humanized Plate 2 Well G03	SAMEA118242640	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 G03\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 G03\|scientific name:Danio rerio	Raw reads: Sample HUM2 G03	webin reads Sample HUM2 G03		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 G03	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G03.R1.fastq.gz G03.R2.fastq.gz	fastq fastq	4967196600.0	16557322.0	webin reads Sample HUM2 G03	0:150 1:150	A:1310441558;C:730142812;G:1820047798;T:1106541425;N:23007	150	150		1310441558	730142812	1820047798	1106541425	23007	ERX14341388	ERS24422814	ERA33115713	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19278	19278	ERR14936818	ERX14341060	ERS24422741	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A02	Humanized Plate 2 Well A02	SAMEA118242567	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 A02\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 A02\|scientific name:Danio rerio	Raw reads: Sample HUM2 A02	webin reads Sample HUM2 A02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 A02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A02.R1.fastq.gz A02.R2.fastq.gz	fastq fastq	3217733700.0	10725779.0	webin reads Sample HUM2 A02	0:150 1:150	A:686575330;C:510490874;G:1381211600;T:639440992;N:14904	150	150		686575330	510490874	1381211600	639440992	14904	ERX14341060	ERS24422741	ERA33115505	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19279	19279	ERR14950774	ERX14354898	ERS24422922	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F07	Knockout Plate Well F07	SAMEA118242748	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO F07\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO F07\|scientific name:Danio rerio	Raw reads: Sample KO F07	webin reads Sample KO F07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO F07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F07.R1.fastq.gz F07.R2.fastq.gz	fastq fastq	10763253300.0	35877511.0	webin reads Sample KO F07	0:150 1:150	A:3904704604;C:1492936538;G:1705278852;T:3660244628;N:88678	150	150		3904704604	1492936538	1705278852	3660244628	88678	ERX14354898	ERS24422922	ERA33121270	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19280	19280	ERR14934968	ERX14339210	ERS24360046	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D01	Humanized Plate 1 Well D01	SAMEA118224969	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 D01\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 D01\|scientific name:Danio rerio	Raw reads: Sample HUM1 D01	webin reads Sample HUM1 D01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 D01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D01.R1.fastq.gz D01.R2.fastq.gz	fastq fastq	169613700.0	565379.0	webin reads Sample HUM1 D01	0:150 1:150	A:44186025;C:22437297;G:59635089;T:43353786;N:1503	150	150		44186025	22437297	59635089	43353786	1503	ERX14339210	ERS24360046	ERA33112474	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19281	19281	ERR14944006	ERX14348158	ERS24422884	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B08	Knockout Plate Well B08	SAMEA118242710	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO B08\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO B08\|scientific name:Danio rerio	Raw reads: Sample KO B08	webin reads Sample KO B08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO B08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B08.R1.fastq.gz B08.R2.fastq.gz	fastq fastq	4374918300.0	14583061.0	webin reads Sample KO B08	0:150 1:150	A:1502989289;C:608306022;G:868547831;T:1395039881;N:35277	150	150		1502989289	608306022	868547831	1395039881	35277	ERX14348158	ERS24422884	ERA33119742	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19282	19282	ERR14935068	ERX14339310	ERS24360079	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F10	Humanized Plate 1 Well F10	SAMEA118225002	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 F10\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 F10\|scientific name:Danio rerio	Raw reads: Sample HUM1 F10	webin reads Sample HUM1 F10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 F10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F10.R1.fastq.gz F10.R2.fastq.gz	fastq fastq	366521100.0	1221737.0	webin reads Sample HUM1 F10	0:150 1:150	A:120362548;C:43174281;G:81935740;T:121045446;N:3085	150	150		120362548	43174281	81935740	121045446	3085	ERX14339310	ERS24360079	ERA33112816	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19283	19283	ERR14935151	ERX14339393	ERS24360105	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H12	Humanized Plate 1 Well H12	SAMEA118225028	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H12\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H12\|scientific name:Danio rerio	Raw reads: Sample HUM1 H12	webin reads Sample HUM1 H12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H12.R1.fastq.gz H12.R2.fastq.gz	fastq fastq	64716600.0	215722.0	webin reads Sample HUM1 H12	0:150 1:150	A:11919103;C:8780603;G:32437007;T:11579359;N:528	150	150		11919103	8780603	32437007	11579359	528	ERX14339393	ERS24360105	ERA33113116	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19284	19284	ERR14950775	ERX14354899	ERS24422923	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F08	Knockout Plate Well F08	SAMEA118242749	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO F08\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO F08\|scientific name:Danio rerio	Raw reads: Sample KO F08	webin reads Sample KO F08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO F08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F08.R1.fastq.gz F08.R2.fastq.gz	fastq fastq	862013100.0	2873377.0	webin reads Sample KO F08	0:150 1:150	A:258529164;C:123157615;G:260317379;T:220001971;N:6971	150	150		258529164	123157615	260317379	220001971	6971	ERX14354899	ERS24422923	ERA33121271	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19285	19285	ERR14934987	ERX14339229	ERS24360050	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D05	Humanized Plate 1 Well D05	SAMEA118224973	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 D05\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 D05\|scientific name:Danio rerio	Raw reads: Sample HUM1 D05	webin reads Sample HUM1 D05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 D05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D05.R1.fastq.gz D05.R2.fastq.gz	fastq fastq	87887400.0	292958.0	webin reads Sample HUM1 D05	0:150 1:150	A:19996165;C:11416204;G:37562812;T:18911751;N:468	150	150		19996165	11416204	37562812	18911751	468	ERX14339229	ERS24360050	ERA33112543	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19286	19286	ERR14950668	ERX14354792	ERS24422898	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C10	Knockout Plate Well C10	SAMEA118242724	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO C10\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO C10\|scientific name:Danio rerio	Raw reads: Sample KO C10	webin reads Sample KO C10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO C10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C10.R1.fastq.gz C10.R2.fastq.gz	fastq fastq	2650018500.0	8833395.0	webin reads Sample KO C10	0:150 1:150	A:944147055;C:380161906;G:445871150;T:879817280;N:21109	150	150		944147055	380161906	445871150	879817280	21109	ERX14354792	ERS24422898	ERA33121163	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19287	19287	ERR14937108	ERX14341352	ERS24422801	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F02	Humanized Plate 2 Well F02	SAMEA118242627	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 F02\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 F02\|scientific name:Danio rerio	Raw reads: Sample HUM2 F02	webin reads Sample HUM2 F02		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 F02	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F02.R1.fastq.gz F02.R2.fastq.gz	fastq fastq	4319451600.0	14398172.0	webin reads Sample HUM2 F02	0:150 1:150	A:1013913720;C:720345672;G:1637113325;T:948057846;N:21037	150	150		1013913720	720345672	1637113325	948057846	21037	ERX14341352	ERS24422801	ERA33115690	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19288	19288	ERR14934840	ERX14339082	ERS24360019	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A10	Humanized Plate 1 Well A10	SAMEA118224942	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 A10\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 A10\|scientific name:Danio rerio	Raw reads: Sample HUM1 A10	webin reads Sample HUM1 A10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 A10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A10.R1.fastq.gz A10.R2.fastq.gz	fastq fastq	55647900.0	185493.0	webin reads Sample HUM1 A10	0:150 1:150	A:8450799;C:7127607;G:31284165;T:8784914;N:415	150	150		8450799	7127607	31284165	8784914	415	ERX14339082	ERS24360019	ERA33112084	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19289	19289	ERR14935132	ERX14339374	ERS24360098	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H05	Humanized Plate 1 Well H05	SAMEA118225021	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 H05\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 H05\|scientific name:Danio rerio	Raw reads: Sample HUM1 H05	webin reads Sample HUM1 H05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 H05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H05.R1.fastq.gz H05.R2.fastq.gz	fastq fastq	161532600.0	538442.0	webin reads Sample HUM1 H05	0:150 1:150	A:46954082;C:18456156;G:50213476;T:45907368;N:1518	150	150		46954082	18456156	50213476	45907368	1518	ERX14339374	ERS24360098	ERA33113034	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19290	19290	ERR14934993	ERX14339235	ERS24360053	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D08	Humanized Plate 1 Well D08	SAMEA118224976	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 D08\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 D08\|scientific name:Danio rerio	Raw reads: Sample HUM1 D08	webin reads Sample HUM1 D08		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 D08	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D08.R1.fastq.gz D08.R2.fastq.gz	fastq fastq	163574400.0	545248.0	webin reads Sample HUM1 D08	0:150 1:150	A:36914350;C:20424845;G:69296209;T:36937661;N:1335	150	150		36914350	20424845	69296209	36937661	1335	ERX14339235	ERS24360053	ERA33112562	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19291	19291	ERR14934860	ERX14339102	ERS24360026	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B05	Humanized Plate 1 Well B05	SAMEA118224949	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B05\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B05\|scientific name:Danio rerio	Raw reads: Sample HUM1 B05	webin reads Sample HUM1 B05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B05.R1.fastq.gz B05.R2.fastq.gz	fastq fastq	104906100.0	349687.0	webin reads Sample HUM1 B05	0:150 1:150	A:27195212;C:13543121;G:38418859;T:25748246;N:662	150	150		27195212	13543121	38418859	25748246	662	ERX14339102	ERS24360026	ERA33112153	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19292	19292	ERR14937153	ERX14341397	ERS24422823	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G12	Humanized Plate 2 Well G12	SAMEA118242649	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 G12\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 G12\|scientific name:Danio rerio	Raw reads: Sample HUM2 G12	webin reads Sample HUM2 G12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 G12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G12.R1.fastq.gz G12.R2.fastq.gz	fastq fastq	4617277800.0	15390926.0	webin reads Sample HUM2 G12	0:150 1:150	A:1158729179;C:728158561;G:1691881391;T:1038487859;N:20810	150	150		1158729179	728158561	1691881391	1038487859	20810	ERX14341397	ERS24422823	ERA33115725	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19293	19293	ERR14943976	ERX14348128	ERS24422873	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A09	Knockout Plate Well A09	SAMEA118242699	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO A09\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO A09\|scientific name:Danio rerio	Raw reads: Sample KO A09	webin reads Sample KO A09		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO A09	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A09.R1.fastq.gz A09.R2.fastq.gz	fastq fastq	7026339600.0	23421132.0	webin reads Sample KO A09	0:150 1:150	A:2584462615;C:932829225;G:1126129540;T:2382863475;N:54745	150	150		2584462615	932829225	1126129540	2382863475	54745	ERX14348128	ERS24422873	ERA33119655	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19294	19294	ERR14934848	ERX14339090	ERS24360022	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B01	Humanized Plate 1 Well B01	SAMEA118224945	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 B01\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 B01\|scientific name:Danio rerio	Raw reads: Sample HUM1 B01	webin reads Sample HUM1 B01		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 B01	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B01.R1.fastq.gz B01.R2.fastq.gz	fastq fastq	75625800.0	252086.0	webin reads Sample HUM1 B01	0:150 1:150	A:11997345;C:9943452;G:40709427;T:12974865;N:711	150	150		11997345	9943452	40709427	12974865	711	ERX14339090	ERS24360022	ERA33112111	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19295	19295	ERR14934832	ERX14339074	ERS24360016	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A07	Humanized Plate 1 Well A07	SAMEA118224939	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 A07\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 A07\|scientific name:Danio rerio	Raw reads: Sample HUM1 A07	webin reads Sample HUM1 A07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 A07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A07.R1.fastq.gz A07.R2.fastq.gz	fastq fastq	69187800.0	230626.0	webin reads Sample HUM1 A07	0:150 1:150	A:12381283;C:7906319;G:37465324;T:11434563;N:311	150	150		12381283	7906319	37465324	11434563	311	ERX14339074	ERS24360016	ERA33112056	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19296	19296	ERR14935010	ERX14339252	ERS24360060	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E03	Humanized Plate 1 Well E03	SAMEA118224983	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 E03\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 E03\|scientific name:Danio rerio	Raw reads: Sample HUM1 E03	webin reads Sample HUM1 E03		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 E03	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E03.R1.fastq.gz E03.R2.fastq.gz	fastq fastq	425713200.0	1419044.0	webin reads Sample HUM1 E03	0:150 1:150	A:136345366;C:51139029;G:106693807;T:131531022;N:3976	150	150		136345366	51139029	106693807	131531022	3976	ERX14339252	ERS24360060	ERA33112619	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19297	19297	ERR14937160	ERX14341404	ERS24422830	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well H07	Humanized Plate 2 Well H07	SAMEA118242656	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 H07\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 H07\|scientific name:Danio rerio	Raw reads: Sample HUM2 H07	webin reads Sample HUM2 H07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 H07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	H07.R1.fastq.gz H07.R2.fastq.gz	fastq fastq	2014913100.0	6716377.0	webin reads Sample HUM2 H07	0:150 1:150	A:411170361;C:304335223;G:896421902;T:402976937;N:8677	150	150		411170361	304335223	896421902	402976937	8677	ERX14341404	ERS24422830	ERA33115735	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19298	19298	ERR14936962	ERX14341204	ERS24422793	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E06	Humanized Plate 2 Well E06	SAMEA118242619	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 E06\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 E06\|scientific name:Danio rerio	Raw reads: Sample HUM2 E06	webin reads Sample HUM2 E06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 E06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E06.R1.fastq.gz E06.R2.fastq.gz	fastq fastq	10133040000.0	33776800.0	webin reads Sample HUM2 E06	0:150 1:150	A:3260003556;C:1412856784;G:2700597066;T:2759534229;N:48365	150	150		3260003556	1412856784	2700597066	2759534229	48365	ERX14341204	ERS24422793	ERA33115605	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19299	19299	ERR14950764	ERX14354888	ERS24422920	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F05	Knockout Plate Well F05	SAMEA118242746	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO F05\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO F05\|scientific name:Danio rerio	Raw reads: Sample KO F05	webin reads Sample KO F05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO F05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F05.R1.fastq.gz F05.R2.fastq.gz	fastq fastq	6748159500.0	22493865.0	webin reads Sample KO F05	0:150 1:150	A:2431257026;C:944096584;G:1125684524;T:2247068351;N:53015	150	150		2431257026	944096584	1125684524	2247068351	53015	ERX14354888	ERS24422920	ERA33121260	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19300	19300	ERR14936821	ERX14341063	ERS24422744	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A05	Humanized Plate 2 Well A05	SAMEA118242570	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 A05\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 A05\|scientific name:Danio rerio	Raw reads: Sample HUM2 A05	webin reads Sample HUM2 A05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 A05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A05.R1.fastq.gz A05.R2.fastq.gz	fastq fastq	3531016500.0	11770055.0	webin reads Sample HUM2 A05	0:150 1:150	A:908506275;C:540353948;G:1299418302;T:782721784;N:16191	150	150		908506275	540353948	1299418302	782721784	16191	ERX14341063	ERS24422744	ERA33115508	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19301	19301	ERR14950698	ERX14354822	ERS24422903	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D03	Knockout Plate Well D03	SAMEA118242729	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO D03\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO D03\|scientific name:Danio rerio	Raw reads: Sample KO D03	webin reads Sample KO D03		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO D03	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D03.R1.fastq.gz D03.R2.fastq.gz	fastq fastq	15044100900.0	50147003.0	webin reads Sample KO D03	0:150 1:150	A:5448629271;C:2142046198;G:2372663075;T:5080644849;N:117507	150	150		5448629271	2142046198	2372663075	5080644849	117507	ERX14354822	ERS24422903	ERA33121193	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19302	19302	ERR14950732	ERX14354856	ERS24422910	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well E07	Knockout Plate Well E07	SAMEA118242736	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO E07\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO E07\|scientific name:Danio rerio	Raw reads: Sample KO E07	webin reads Sample KO E07		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO E07	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	E07.R1.fastq.gz E07.R2.fastq.gz	fastq fastq	12898175700.0	42993919.0	webin reads Sample KO E07	0:150 1:150	A:4589735008;C:1839814686;G:2098030544;T:4370493808;N:101654	150	150		4589735008	1839814686	2098030544	4370493808	101654	ERX14354856	ERS24422910	ERA33121227	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19303	19303	ERR14934842	ERX14339084	ERS24360020	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A11	Humanized Plate 1 Well A11	SAMEA118224943	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 A11\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 A11\|scientific name:Danio rerio	Raw reads: Sample HUM1 A11	webin reads Sample HUM1 A11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 A11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A11.R1.fastq.gz A11.R2.fastq.gz	fastq fastq	53858400.0	179528.0	webin reads Sample HUM1 A11	0:150 1:150	A:12307549;C:6368678;G:23753869;T:11428030;N:274	150	150		12307549	6368678	23753869	11428030	274	ERX14339084	ERS24360020	ERA33112092	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19304	19304	ERR14950672	ERX14354796	ERS24422899	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well C11	Knockout Plate Well C11	SAMEA118242725	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO C11\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO C11\|scientific name:Danio rerio	Raw reads: Sample KO C11	webin reads Sample KO C11		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO C11	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	C11.R1.fastq.gz C11.R2.fastq.gz	fastq fastq	6484306200.0	21614354.0	webin reads Sample KO C11	0:150 1:150	A:2345044923;C:858634350;G:1122803400;T:2157772266;N:51261	150	150		2345044923	858634350	1122803400	2157772266	51261	ERX14354796	ERS24422899	ERA33121167	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19305	19305	ERR14934989	ERX14339231	ERS24360051	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well D06	Humanized Plate 1 Well D06	SAMEA118224974	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 D06\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 D06\|scientific name:Danio rerio	Raw reads: Sample HUM1 D06	webin reads Sample HUM1 D06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 D06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	D06.R1.fastq.gz D06.R2.fastq.gz	fastq fastq	110618100.0	368727.0	webin reads Sample HUM1 D06	0:150 1:150	A:26616860;C:14643839;G:43583750;T:25772923;N:728	150	150		26616860	14643839	43583750	25772923	728	ERX14339231	ERS24360051	ERA33112549	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19306	19306	ERR14950801	ERX14354925	ERS24422933	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G06	Knockout Plate Well G06	SAMEA118242759	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO G06\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO G06\|scientific name:Danio rerio	Raw reads: Sample KO G06	webin reads Sample KO G06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO G06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G06.R1.fastq.gz G06.R2.fastq.gz	fastq fastq	1620231000.0	5400770.0	webin reads Sample KO G06	0:150 1:150	A:552572070;C:218631707;G:363017635;T:485997489;N:12099	150	150		552572070	218631707	363017635	485997489	12099	ERX14354925	ERS24422933	ERA33121297	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19307	19307	ERR14936889	ERX14341131	ERS24422756	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well B05	Humanized Plate 2 Well B05	SAMEA118242582	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 B05\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 B05\|scientific name:Danio rerio	Raw reads: Sample HUM2 B05	webin reads Sample HUM2 B05		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 B05	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	B05.R1.fastq.gz B05.R2.fastq.gz	fastq fastq	9672318000.0	32241060.0	webin reads Sample HUM2 B05	0:150 1:150	A:3355070462;C:1344914308;G:2133672630;T:2838610016;N:50584	150	150		3355070462	1344914308	2133672630	2838610016	50584	ERX14341131	ERS24422756	ERA33115569	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19308	19308	ERR14936826	ERX14341068	ERS24422749	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well A10	Humanized Plate 2 Well A10	SAMEA118242575	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 A10\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 A10\|scientific name:Danio rerio	Raw reads: Sample HUM2 A10	webin reads Sample HUM2 A10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 A10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	A10.R1.fastq.gz A10.R2.fastq.gz	fastq fastq	3319486500.0	11064955.0	webin reads Sample HUM2 A10	0:150 1:150	A:667756780;C:505774653;G:1498623562;T:647316121;N:15384	150	150		667756780	505774653	1498623562	647316121	15384	ERX14341068	ERS24422749	ERA33115516	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19309	19309	ERR14950797	ERX14354921	ERS24422931	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G04	Knockout Plate Well G04	SAMEA118242757	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO G04\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO G04\|scientific name:Danio rerio	Raw reads: Sample KO G04	webin reads Sample KO G04		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO G04	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G04.R1.fastq.gz G04.R2.fastq.gz	fastq fastq	1169241600.0	3897472.0	webin reads Sample KO G04	0:150 1:150	A:414405945;C:160380699;G:232288284;T:362157277;N:9395	150	150		414405945	160380699	232288284	362157277	9395	ERX14354921	ERS24422931	ERA33121293	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19310	19310	ERR14935076	ERX14339318	ERS24360081	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well F12	Humanized Plate 1 Well F12	SAMEA118225004	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM1 F12\|collection date:2022 11 14\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM1 F12\|scientific name:Danio rerio	Raw reads: Sample HUM1 F12	webin reads Sample HUM1 F12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM1 F12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	F12.R1.fastq.gz F12.R2.fastq.gz	fastq fastq	460315800.0	1534386.0	webin reads Sample HUM1 F12	0:150 1:150	A:151663513;C:57564329;G:101614217;T:149469927;N:3814	150	150		151663513	57564329	101614217	149469927	3814	ERX14339318	ERS24360081	ERA33112847	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19311	19311	ERR14950818	ERX14354942	ERS24422939	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G12	Knockout Plate Well G12	SAMEA118242765	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO G12\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO G12\|scientific name:Danio rerio	Raw reads: Sample KO G12	webin reads Sample KO G12		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO G12	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G12.R1.fastq.gz G12.R2.fastq.gz	fastq fastq	413542200.0	1378474.0	webin reads Sample KO G12	0:150 1:150	A:126933895;C:59697863;G:113997315;T:112909944;N:3183	150	150		126933895	59697863	113997315	112909944	3183	ERX14354942	ERS24422939	ERA33121314	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19312	19312	ERR14950814	ERX14354938	ERS24422937	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G10	Knockout Plate Well G10	SAMEA118242763	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample KO G10\|collection date:2022 05 13\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample KO G10\|scientific name:Danio rerio	Raw reads: Sample KO G10	webin reads Sample KO G10		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample KO G10	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G10.R1.fastq.gz G10.R2.fastq.gz	fastq fastq	4954517100.0	16515057.0	webin reads Sample KO G10	0:150 1:150	A:1782759867;C:666395120;G:897330151;T:1607991435;N:40527	150	150		1782759867	666395120	897330151	1607991435	40527	ERX14354938	ERS24422937	ERA33121310	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System
19313	19313	ERR14937147	ERX14341391	ERS24422817	ERP166068	PRJEB82358	Human gene duplications	53f6d331-4985-4b69-8ac3-a57d010118dd	Other	Duplicated genes expanded in the human lineage likely contributed to brain evolution yet challenges exist in their discovery due to sequence assembly errors. We used a complete telomere to telomere genome sequence to identify 213 human specific gene families. From these 362 paralogs were found in all modern human genomes tested and brain transcriptomes making them top candidates contributing to human universal brain features. Choosing a subset of paralogs we used long read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development we generated zebrafish CRISPR “knockout” models of nine orthologs and introduced mRNA encoding paralogs effectively “humanizing” larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	Single cell RNA sequencing of zebrafish heads from well G06	Humanized Plate 2 Well G06	SAMEA118242643	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 05 23\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample HUM2 G06\|collection date:2022 12 21\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample HUM2 G06\|scientific name:Danio rerio	Raw reads: Sample HUM2 G06	webin reads Sample HUM2 G06		unspecified		ENA STATUS ID:4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP166068	Raw reads: Sample HUM2 G06	ENA STATUS ID:4\|ENA FIRST PUBLIC:2025 05 23\|ENA LAST UPDATE:2025 05 23	G06.R1.fastq.gz G06.R2.fastq.gz	fastq fastq	2593562100.0	8645207.0	webin reads Sample HUM2 G06	0:150 1:150	A:506680806;C:379714116;G:1209306962;T:497848288;N:11928	150	150		506680806	379714116	1209306962	497848288	11928	ERX14341391	ERS24422817	ERA33115717	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS												T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-05-23	Larval	Larval	Head	Nervous System

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