metadata: run_metadata: 157 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue_curation

157 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
25091	25091	SRR25567703	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L001_R1_001.fastq.gz	fastq	445428400.0	5860900.0	GSM7696246 r1	0:76	A:143568074;C:79903177;G:79677344;T:142230186;N:49619	76	143568074	79903177	79677344	142230186	49619	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75644	0.67481	0.78062	0.49002	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25092	25092	SRR25567704	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L002_R1_001.fastq.gz	fastq	436280280.0	5740530.0	GSM7696246 r2	0:76	A:140668025;C:78248456;G:77919880;T:139381210;N:62709	76	140668025	78248456	77919880	139381210	62709	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75737	0.67543	0.77796	0.494	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25093	25093	SRR25567705	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L003_R1_001.fastq.gz	fastq	453115800.0	5962050.0	GSM7696246 r3	0:76	A:145977328;C:81331359;G:81042932;T:144726596;N:37585	76	145977328	81331359	81042932	144726596	37585	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75941	0.67812	0.78255	0.49198	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25094	25094	SRR25567706	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L004_R1_001.fastq.gz	fastq	451629316.0	5942491.0	GSM7696246 r4	0:76	A:145539227;C:81081378;G:80692220;T:144283694;N:32797	76	145539227	81081378	80692220	144283694	32797	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75907	0.67763	0.78074	0.49757	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25095	25095	SRR25567707	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L001_R1_001.fastq.gz	fastq	438903344.0	5775044.0	GSM7696245 r1	0:76	A:141636851;C:79318996;G:78779375;T:139120411;N:47711	76	141636851	79318996	78779375	139120411	47711	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.76357	0.65866	0.76238	0.48958	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25096	25096	SRR25567708	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L002_R1_001.fastq.gz	fastq	429344216.0	5649266.0	GSM7696245 r2	0:76	A:138620131;C:77579442;G:76950101;T:136131396;N:63146	76	138620131	77579442	76950101	136131396	63146	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.76216	0.65728	0.76132	0.4958	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25097	25097	SRR25567709	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L003_R1_001.fastq.gz	fastq	446301792.0	5872392.0	GSM7696245 r3	0:76	A:143941333;C:80689335;G:80111561;T:141523625;N:35938	76	143941333	80689335	80111561	141523625	35938	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.76416	0.65858	0.76177	0.48634	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25098	25098	SRR25567710	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L004_R1_001.fastq.gz	fastq	443971252.0	5841727.0	GSM7696245 r4	0:76	A:143197029;C:80287228;G:79639533;T:140816381;N:31081	76	143197029	80287228	79639533	140816381	31081	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77093	0.66467	0.76081	0.49407	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25099	25099	SRR25567711	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L001_R1_001.fastq.gz	fastq	392537796.0	5164971.0	GSM7696244 r1	0:76	A:124144181;C:72762157;G:72562894;T:123025322;N:43242	76	124144181	72762157	72562894	123025322	43242	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.78106	0.59772	0.73553	0.48949	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25100	25100	SRR25567712	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L002_R1_001.fastq.gz	fastq	384487572.0	5059047.0	GSM7696244 r2	0:76	A:121620414;C:71266999;G:70967086;T:120577709;N:55364	76	121620414	71266999	70967086	120577709	55364	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77986	0.59517	0.73547	0.48651	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25101	25101	SRR25567713	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L003_R1_001.fastq.gz	fastq	399939360.0	5262360.0	GSM7696244 r3	0:76	A:126400057;C:74196301;G:73931308;T:125379595;N:32099	76	126400057	74196301	73931308	125379595	32099	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77917	0.59465	0.7359	0.48952	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25102	25102	SRR25567714	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L004_R1_001.fastq.gz	fastq	398035712.0	5237312.0	GSM7696244 r4	0:76	A:125843687;C:73845902;G:73489490;T:124828195;N:28438	76	125843687	73845902	73489490	124828195	28438	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77934	0.59613	0.73608	0.48475	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25103	25103	SRR25567715	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L001_R1_001.fastq.gz	fastq	412291944.0	5424894.0	GSM7696243 r1	0:76	A:129182868;C:77123147;G:77053023;T:128887593;N:45313	76	129182868	77123147	77053023	128887593	45313	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.79085	0.52962	0.7349	0.48594	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25104	25104	SRR25567716	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L002_R1_001.fastq.gz	fastq	404294768.0	5319668.0	GSM7696243 r2	0:76	A:126685179;C:75658897;G:75455501;T:126437486;N:57705	76	126685179	75658897	75455501	126437486	57705	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.79163	0.52938	0.73304	0.48118	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25105	25105	SRR25567717	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L003_R1_001.fastq.gz	fastq	419693128.0	5522278.0	GSM7696243 r3	0:76	A:131491219;C:78551884;G:78434940;T:131179828;N:35257	76	131491219	78551884	78434940	131179828	35257	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.79077	0.52836	0.73419	0.48215	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25106	25106	SRR25567718	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.	pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L004_R1_001.fastq.gz	fastq	418155268.0	5502043.0	GSM7696243 r4	0:76	A:130978746;C:78285682;G:78062725;T:130798846;N:29269	76	130978746	78285682	78062725	130798846	29269	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.78728	0.52541	0.73484	0.48813	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
29894	29894	SRR30873028	SRX26270368	SRS22808226	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep15	GSM8553345	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep15	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types	GSM8553345	GSM8553345: arid1b 6 dpf rep15; Danio rerio; RNA Seq	GSM8553345 r1	GSM8553345	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-wt_AR28_S28_R1_001.fastq.gz	fastq	4135380800.0	41353808.0	GSM8553345 r1	0:100	A:1084939463;C:1011079577;G:970891275;T:1068398012;N:72473	100	1084939463	1011079577	970891275	1068398012	72473	SRX26270368	SRS22808226	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29895	29895	SRR30873029	SRX26270367	SRS22808225	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep14	GSM8553344	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep14	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types	GSM8553344	GSM8553344: arid1b 6 dpf rep14; Danio rerio; RNA Seq	GSM8553344 r1	GSM8553344	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-wt_AR27_S27_R1_001.fastq.gz	fastq	6224312000.0	62243120.0	GSM8553344 r1	0:100	A:1606079574;C:1540033115;G:1483199092;T:1594888859;N:111360	100	1606079574	1540033115	1483199092	1594888859	111360	SRX26270367	SRS22808225	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29896	29896	SRR30873030	SRX26270366	SRS22808224	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep13	GSM8553343	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep13	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types	GSM8553343	GSM8553343: arid1b 6 dpf rep13; Danio rerio; RNA Seq	GSM8553343 r1	GSM8553343	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-wt_AR26_S26_R1_001.fastq.gz	fastq	4549812900.0	45498129.0	GSM8553343 r1	0:100	A:1188852707;C:1130004381;G:1033560381;T:1197314769;N:80662	100	1188852707	1130004381	1033560381	1197314769	80662	SRX26270366	SRS22808224	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29897	29897	SRR30873031	SRX26270365	SRS22808223	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep12	GSM8553342	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep12	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types	GSM8553342	GSM8553342: arid1b 6 dpf rep12; Danio rerio; RNA Seq	GSM8553342 r1	GSM8553342	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-wt_AR25_S25_R1_001.fastq.gz	fastq	4879728400.0	48797284.0	GSM8553342 r1	0:100	A:1257198257;C:1231843411;G:1157132375;T:1233469179;N:85178	100	1257198257	1231843411	1157132375	1233469179	85178	SRX26270365	SRS22808223	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29898	29898	SRR30873032	SRX26270364	SRS22808222	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep11	GSM8553341	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i wild types	GSM8553341	GSM8553341: arid1b 6 dpf rep11; Danio rerio; RNA Seq	GSM8553341 r1	GSM8553341	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-wt_AR24_S24_R1_001.fastq.gz	fastq	4082165400.0	40821654.0	GSM8553341 r1	0:100	A:1040984378;C:1022942149;G:978845633;T:1039318707;N:74533	100	1040984378	1022942149	978845633	1039318707	74533	SRX26270364	SRS22808222	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29899	29899	SRR30873033	SRX26270363	SRS22808221	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep10	GSM8553340	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous	GSM8553340	GSM8553340: arid1b 6 dpf rep10; Danio rerio; RNA Seq	GSM8553340 r1	GSM8553340	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-hom_AR23_S23_R1_001.fastq.gz	fastq	4661017700.0	46610177.0	GSM8553340 r1	0:100	A:1238725482;C:1138186288;G:1061058641;T:1222964445;N:82844	100	1238725482	1138186288	1061058641	1222964445	82844	SRX26270363	SRS22808221	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29900	29900	SRR30873034	SRX26270362	SRS22808220	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep9	GSM8553339	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous	GSM8553339	GSM8553339: arid1b 6 dpf rep9; Danio rerio; RNA Seq	GSM8553339 r1	GSM8553339	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-hom_AR22_S22_R1_001.fastq.gz	fastq	4221752400.0	42217524.0	GSM8553339 r1	0:100	A:1065652742;C:1071696614;G:1016007642;T:1068321142;N:74260	100	1065652742	1071696614	1016007642	1068321142	74260	SRX26270362	SRS22808220	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29901	29901	SRR30873035	SRX26270361	SRS22808219	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep8	GSM8553338	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous	GSM8553338	GSM8553338: arid1b 6 dpf rep8; Danio rerio; RNA Seq	GSM8553338 r1	GSM8553338	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-hom_AR21_S21_R1_001.fastq.gz	fastq	4432057900.0	44320579.0	GSM8553338 r1	0:100	A:1141942260;C:1108384050;G:1058194972;T:1123456708;N:79910	100	1141942260	1108384050	1058194972	1123456708	79910	SRX26270361	SRS22808219	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29902	29902	SRR30873036	SRX26270360	SRS22808218	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep7	GSM8553337	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous	GSM8553337	GSM8553337: arid1b 6 dpf rep7; Danio rerio; RNA Seq	GSM8553337 r1	GSM8553337	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-hom_AR20_S20_R1_001.fastq.gz	fastq	4445102100.0	44451021.0	GSM8553337 r1	0:100	A:1155131497;C:1102948564;G:1044423066;T:1142521451;N:77522	100	1155131497	1102948564	1044423066	1142521451	77522	SRX26270360	SRS22808218	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29903	29903	SRR30873037	SRX26270359	SRS22808217	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep6	GSM8553336	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i homozygous	GSM8553336	GSM8553336: arid1b 6 dpf rep6; Danio rerio; RNA Seq	GSM8553336 r1	GSM8553336	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-hom_AR19_S19_R1_001.fastq.gz	fastq	4466739200.0	44667392.0	GSM8553336 r1	0:100	A:1142963908;C:1130243443;G:1069626640;T:1123824589;N:80620	100	1142963908	1130243443	1069626640	1123824589	80620	SRX26270359	SRS22808217	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29904	29904	SRR30873038	SRX26270358	SRS22808216	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep5	GSM8553335	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous	GSM8553335	GSM8553335: arid1b 6 dpf rep5; Danio rerio; RNA Seq	GSM8553335 r1	GSM8553335	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-het_AR18_S18_R1_001.fastq.gz	fastq	3870464200.0	38704642.0	GSM8553335 r1	0:100	A:1000259085;C:960215025;G:917241491;T:992680013;N:68586	100	1000259085	960215025	917241491	992680013	68586	SRX26270358	SRS22808216	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29905	29905	SRR30873039	SRX26270357	SRS22808215	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep4	GSM8553334	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous	GSM8553334	GSM8553334: arid1b 6 dpf rep4; Danio rerio; RNA Seq	GSM8553334 r1	GSM8553334	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-het_AR17_S17_R1_001.fastq.gz	fastq	4594184100.0	45941841.0	GSM8553334 r1	0:100	A:1184283243;C:1151731213;G:1096934508;T:1161152565;N:82571	100	1184283243	1151731213	1096934508	1161152565	82571	SRX26270357	SRS22808215	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29906	29906	SRR30873040	SRX26270356	SRS22808214	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep3	GSM8553333	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous	GSM8553333	GSM8553333: arid1b 6 dpf rep3; Danio rerio; RNA Seq	GSM8553333 r1	GSM8553333	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-het_AR16_S16_R1_001.fastq.gz	fastq	4941522000.0	49415220.0	GSM8553333 r1	0:100	A:1259383920;C:1247709712;G:1186755788;T:1247582989;N:89591	100	1259383920	1247709712	1186755788	1247582989	89591	SRX26270356	SRS22808214	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29907	29907	SRR30873041	SRX26270355	SRS22808213	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep2	GSM8553332	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous	GSM8553332	GSM8553332: arid1b 6 dpf rep2; Danio rerio; RNA Seq	GSM8553332 r1	GSM8553332	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-het_AR15_S15_R1_001.fastq.gz	fastq	4104651300.0	41046513.0	GSM8553332 r1	0:100	A:1076649631;C:1007609502;G:973534133;T:1046799245;N:58789	100	1076649631	1007609502	973534133	1046799245	58789	SRX26270355	SRS22808213	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29908	29908	SRR30873042	SRX26270354	SRS22808212	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		arid1b 6 dpf rep1	GSM8553331	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous\|geo loc name:missing\|collection date:missing	arid1b 6 dpf rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:arid1b 195d50i heterozygous	GSM8553331	GSM8553331: arid1b 6 dpf rep1; Danio rerio; RNA Seq	GSM8553331 r1	GSM8553331	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215		arid1b-195d50i-het_AR14_S14_R1_001.fastq.gz	fastq	2182363600.0	21823636.0	GSM8553331 r1	0:100	A:567445925;C:541275778;G:507884278;T:565718419;N:39200	100	567445925	541275778	507884278	565718419	39200	SRX26270354	SRS22808212	SRA1985473	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-10-03	Larval	Larval	Multi-tissue	Multi-system
29909	29909	SRR27592934	SRX23261746	SRS20163710	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep11	GSM8020192	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020192	GSM8020192: deaf1 2 dpf rep11; Danio rerio; RNA Seq	GSM8020192 r1	GSM8020192	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-wt_D28_S56_R1_001.fastq.gz	fastq	4475806200.0	44758062.0	GSM8020192 r1	0:100	A:1106171674;C:1156870042;G:1092472583;T:1120212338;N:79563	100	1106171674	1156870042	1092472583	1120212338	79563	SRX23261746	SRS20163710	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29910	29910	SRR27592935	SRX23261745	SRS20163711	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep10	GSM8020191	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020191	GSM8020191: deaf1 2 dpf rep10; Danio rerio; RNA Seq	GSM8020191 r1	GSM8020191	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-wt_D27_S55_R1_001.fastq.gz	fastq	4001586700.0	40015867.0	GSM8020191 r1	0:100	A:1000059012;C:1020300240;G:981249122;T:999909425;N:68901	100	1000059012	1020300240	981249122	999909425	68901	SRX23261745	SRS20163711	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29911	29911	SRR27592936	SRX23261744	SRS20163709	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep9	GSM8020190	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020190	GSM8020190: deaf1 2 dpf rep9; Danio rerio; RNA Seq	GSM8020190 r1	GSM8020190	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-wt_D26_S54_R1_001.fastq.gz	fastq	3716740300.0	37167403.0	GSM8020190 r1	0:100	A:930732486;C:940157658;G:908687307;T:937097122;N:65727	100	930732486	940157658	908687307	937097122	65727	SRX23261744	SRS20163709	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29912	29912	SRR27592937	SRX23261743	SRS20163708	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep8	GSM8020189	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020189	GSM8020189: deaf1 2 dpf rep8; Danio rerio; RNA Seq	GSM8020189 r1	GSM8020189	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-hom_D25_S53_R1_001.fastq.gz	fastq	3741485000.0	37414850.0	GSM8020189 r1	0:100	A:929440558;C:958986044;G:914039968;T:938952561;N:65869	100	929440558	958986044	914039968	938952561	65869	SRX23261743	SRS20163708	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29913	29913	SRR27592938	SRX23261742	SRS20163707	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep7	GSM8020188	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020188	GSM8020188: deaf1 2 dpf rep7; Danio rerio; RNA Seq	GSM8020188 r1	GSM8020188	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-hom_D24_S52_R1_001.fastq.gz	fastq	2971991400.0	29719914.0	GSM8020188 r1	0:100	A:738636815;C:755836125;G:729168292;T:748297854;N:52314	100	738636815	755836125	729168292	748297854	52314	SRX23261742	SRS20163707	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29914	29914	SRR27592939	SRX23261741	SRS20163706	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep6	GSM8020187	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020187	GSM8020187: deaf1 2 dpf rep6; Danio rerio; RNA Seq	GSM8020187 r1	GSM8020187	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-hom_D23_S51_R1_001.fastq.gz	fastq	4134397800.0	41343978.0	GSM8020187 r1	0:100	A:1032735373;C:1051188374;G:1016197596;T:1034203095;N:73362	100	1032735373	1051188374	1016197596	1034203095	73362	SRX23261741	SRS20163706	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29915	29915	SRR27592940	SRX23261740	SRS20163705	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep5	GSM8020186	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020186	GSM8020186: deaf1 2 dpf rep5; Danio rerio; RNA Seq	GSM8020186 r1	GSM8020186	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-hom_D22_S50_R1_001.fastq.gz	fastq	3631624500.0	36316245.0	GSM8020186 r1	0:100	A:901094303;C:929956244;G:893844528;T:906664233;N:65192	100	901094303	929956244	893844528	906664233	65192	SRX23261740	SRS20163705	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29916	29916	SRR27592941	SRX23261739	SRS20163704	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep4	GSM8020185	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020185	GSM8020185: deaf1 2 dpf rep4; Danio rerio; RNA Seq	GSM8020185 r1	GSM8020185	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-hom_D21_S49_R1_001.fastq.gz	fastq	3349609200.0	33496092.0	GSM8020185 r1	0:100	A:835857971;C:854981364;G:824035698;T:834673793;N:60374	100	835857971	854981364	824035698	834673793	60374	SRX23261739	SRS20163704	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29917	29917	SRR27592942	SRX23261738	SRS20163703	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep3	GSM8020184	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous	GSM8020184	GSM8020184: deaf1 2 dpf rep3; Danio rerio; RNA Seq	GSM8020184 r1	GSM8020184	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-het_D20_S48_R1_001.fastq.gz	fastq	3371713300.0	33717133.0	GSM8020184 r1	0:100	A:839050016;C:857965663;G:828869795;T:845766740;N:61086	100	839050016	857965663	828869795	845766740	61086	SRX23261738	SRS20163703	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29918	29918	SRR27592943	SRX23261737	SRS20163701	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep2	GSM8020183	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous	GSM8020183	GSM8020183: deaf1 2 dpf rep2; Danio rerio; RNA Seq	GSM8020183 r1	GSM8020183	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-het_D18_S46_R1_001.fastq.gz	fastq	3756501100.0	37565011.0	GSM8020183 r1	0:100	A:938612608;C:949004833;G:927692516;T:941125085;N:66058	100	938612608	949004833	927692516	941125085	66058	SRX23261737	SRS20163701	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29919	29919	SRR27592944	SRX23261736	SRS20163702	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 2 dpf rep1	GSM8020182	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous\|geo loc name:missing\|collection date:missing	deaf1 2 dpf rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous	GSM8020182	GSM8020182: deaf1 2 dpf rep1; Danio rerio; RNA Seq	GSM8020182 r1	GSM8020182	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-2dpf-het_D17_S45_R1_001.fastq.gz	fastq	3378074100.0	33780741.0	GSM8020182 r1	0:100	A:839320911;C:859028175;G:836373251;T:843291522;N:60241	100	839320911	859028175	836373251	843291522	60241	SRX23261736	SRS20163702	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29920	29920	SRR27592945	SRX23261735	SRS20163699	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep13	GSM8020181	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep13	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types	GSM8020181	GSM8020181: deaf1 t238p 2 dpf rep13; Danio rerio; RNA Seq	GSM8020181 r1	GSM8020181	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-wt_ST4.fastq.gz	fastq	2522881653.0	33818740.0	GSM8020181 r1	0:74.60	A:655207900;C:616856238;G:613068980;T:637525231;N:223304	74	655207900	616856238	613068980	637525231	223304	SRX23261735	SRS20163699	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29921	29921	SRR27592946	SRX23261734	SRS20163698	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep12	GSM8020180	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep12	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types	GSM8020180	GSM8020180: deaf1 t238p 2 dpf rep12; Danio rerio; RNA Seq	GSM8020180 r1	GSM8020180	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-wt_ST3.fastq.gz	fastq	3232696302.0	43332777.0	GSM8020180 r1	0:74.60	A:838706781;C:792017578;G:780975426;T:820709157;N:287360	74	838706781	792017578	780975426	820709157	287360	SRX23261734	SRS20163698	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29922	29922	SRR27592947	SRX23261733	SRS20163700	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep11	GSM8020179	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types	GSM8020179	GSM8020179: deaf1 t238p 2 dpf rep11; Danio rerio; RNA Seq	GSM8020179 r1	GSM8020179	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-wt_ST2.fastq.gz	fastq	3105671470.0	41634840.0	GSM8020179 r1	0:74.59	A:797054679;C:770109006;G:759275000;T:778955169;N:277616	74	797054679	770109006	759275000	778955169	277616	SRX23261733	SRS20163700	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29923	29923	SRR27592948	SRX23261732	SRS20163697	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep10	GSM8020178	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p wild types	GSM8020178	GSM8020178: deaf1 t238p 2 dpf rep10; Danio rerio; RNA Seq	GSM8020178 r1	GSM8020178	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-wt_ST1.fastq.gz	fastq	3499217864.0	46905154.0	GSM8020178 r1	0:74.60	A:893360259;C:869418642;G:860403580;T:875711902;N:323481	74	893360259	869418642	860403580	875711902	323481	SRX23261732	SRS20163697	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29924	29924	SRR27592949	SRX23261731	SRS20163696	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep9	GSM8020177	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous	GSM8020177	GSM8020177: deaf1 t238p 2 dpf rep9; Danio rerio; RNA Seq	GSM8020177 r1	GSM8020177	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-hom_ST8.fastq.gz	fastq	3268771798.0	43820118.0	GSM8020177 r1	0:74.60	A:847366551;C:800849702;G:791226044;T:829037606;N:291895	74	847366551	800849702	791226044	829037606	291895	SRX23261731	SRS20163696	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29925	29925	SRR27592950	SRX23261730	SRS20163695	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep8	GSM8020176	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous	GSM8020176	GSM8020176: deaf1 t238p 2 dpf rep8; Danio rerio; RNA Seq	GSM8020176 r1	GSM8020176	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-hom_ST7.fastq.gz	fastq	2027174325.0	27178466.0	GSM8020176 r1	0:74.59	A:525317640;C:498055852;G:491357881;T:512263813;N:179139	74	525317640	498055852	491357881	512263813	179139	SRX23261730	SRS20163695	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29926	29926	SRR27592951	SRX23261729	SRS20163694	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep7	GSM8020175	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous	GSM8020175	GSM8020175: deaf1 t238p 2 dpf rep7; Danio rerio; RNA Seq	GSM8020175 r1	GSM8020175	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-hom_ST6.fastq.gz	fastq	2787340348.0	37363599.0	GSM8020175 r1	0:74.60	A:722896986;C:681138747;G:674833627;T:708219281;N:251707	74	722896986	681138747	674833627	708219281	251707	SRX23261729	SRS20163694	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29927	29927	SRR27592952	SRX23261728	SRS20163693	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep6	GSM8020174	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p homozygous	GSM8020174	GSM8020174: deaf1 t238p 2 dpf rep6; Danio rerio; RNA Seq	GSM8020174 r1	GSM8020174	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-hom_ST5.fastq.gz	fastq	2977171544.0	39908640.0	GSM8020174 r1	0:74.60	A:770250088;C:731344480;G:721594408;T:753713587;N:268981	74	770250088	731344480	721594408	753713587	268981	SRX23261728	SRS20163693	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29928	29928	SRR27592953	SRX23261727	SRS20163692	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep5	GSM8020173	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous	GSM8020173	GSM8020173: deaf1 t238p 2 dpf rep5; Danio rerio; RNA Seq	GSM8020173 r1	GSM8020173	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-het_ST9.fastq.gz	fastq	2546529762.0	34141024.0	GSM8020173 r1	0:74.59	A:665391714;C:618921995;G:614059292;T:647931593;N:225168	74	665391714	618921995	614059292	647931593	225168	SRX23261727	SRS20163692	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29929	29929	SRR27592954	SRX23261726	SRS20163691	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep4	GSM8020172	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous	GSM8020172	GSM8020172: deaf1 t238p 2 dpf rep4; Danio rerio; RNA Seq	GSM8020172 r1	GSM8020172	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-het_ST13.fastq.gz	fastq	3176861738.0	42588753.0	GSM8020172 r1	0:74.59	A:831927955;C:768758728;G:763547713;T:812339162;N:288180	74	831927955	768758728	763547713	812339162	288180	SRX23261726	SRS20163691	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29930	29930	SRR27592955	SRX23261725	SRS20163690	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep3	GSM8020171	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous	GSM8020171	GSM8020171: deaf1 t238p 2 dpf rep3; Danio rerio; RNA Seq	GSM8020171 r1	GSM8020171	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-het_ST12.fastq.gz	fastq	1136232560.0	15234548.0	GSM8020171 r1	0:74.58	A:297385645;C:276022399;G:273402666;T:289320311;N:101539	74	297385645	276022399	273402666	289320311	101539	SRX23261725	SRS20163690	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29931	29931	SRR27592956	SRX23261724	SRS20163689	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep2	GSM8020170	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous	GSM8020170	GSM8020170: deaf1 t238p 2 dpf rep2; Danio rerio; RNA Seq	GSM8020170 r1	GSM8020170	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-het_ST11.fastq.gz	fastq	2735749019.0	36680185.0	GSM8020170 r1	0:74.58	A:721197113;C:659588175;G:652875625;T:701848626;N:239480	74	721197113	659588175	652875625	701848626	239480	SRX23261724	SRS20163689	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29932	29932	SRR27592957	SRX23261723	SRS20163688	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 t238p 2 dpf rep1	GSM8020169	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous\|geo loc name:missing\|collection date:missing	deaf1 t238p 2 dpf rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 t238p heterozygous	GSM8020169	GSM8020169: deaf1 t238p 2 dpf rep1; Danio rerio; RNA Seq	GSM8020169 r1	GSM8020169	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP484215		deaf1-t238p-2dpf-het_ST10.fastq.gz	fastq	3369699901.0	45178398.0	GSM8020169 r1	0:74.59	A:883991145;C:814741172;G:809532162;T:861133903;N:301519	74	883991145	814741172	809532162	861133903	301519	SRX23261723	SRS20163688	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29947	29947	SRR27592972	SRX23261708	SRS20163673	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep13	GSM8020168	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep13	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types	GSM8020168	GSM8020168: deaf1 c207y 2 dpf rep13; Danio rerio; RNA Seq	GSM8020168 r1	GSM8020168	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-wt_B2_S14_R1_001.fastq.gz	fastq	2963811367.0	29344667.0	GSM8020168 r1	0:101	A:803333990;C:685431342;G:677569210;T:797384558;N:92267	101	803333990	685431342	677569210	797384558	92267	SRX23261708	SRS20163673	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29948	29948	SRR27592973	SRX23261707	SRS20163672	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep12	GSM8020167	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep12	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types	GSM8020167	GSM8020167: deaf1 c207y 2 dpf rep12; Danio rerio; RNA Seq	GSM8020167 r1	GSM8020167	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-wt_B1_S13_R1_001.fastq.gz	fastq	3184165289.0	31526389.0	GSM8020167 r1	0:101	A:847208990;C:751109498;G:736855605;T:848892893;N:98303	101	847208990	751109498	736855605	848892893	98303	SRX23261707	SRS20163672	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29949	29949	SRR27592974	SRX23261706	SRS20163671	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep11	GSM8020166	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types	GSM8020166	GSM8020166: deaf1 c207y 2 dpf rep11; Danio rerio; RNA Seq	GSM8020166 r1	GSM8020166	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-wt_A12_S12_R1_001.fastq.gz	fastq	3115838183.0	30849883.0	GSM8020166 r1	0:101	A:846133299;C:724401184;G:709966835;T:835240904;N:95961	101	846133299	724401184	709966835	835240904	95961	SRX23261706	SRS20163671	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29950	29950	SRR27592975	SRX23261705	SRS20163670	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep10	GSM8020165	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types	GSM8020165	GSM8020165: deaf1 c207y 2 dpf rep10; Danio rerio; RNA Seq	GSM8020165 r1	GSM8020165	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-wt_A11_S11_R1_001.fastq.gz	fastq	2767984184.0	27405784.0	GSM8020165 r1	0:101	A:753665483;C:638171516;G:626255827;T:749805524;N:85834	101	753665483	638171516	626255827	749805524	85834	SRX23261705	SRS20163670	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29951	29951	SRR27592976	SRX23261704	SRS20163669	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep9	GSM8020164	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y wild types	GSM8020164	GSM8020164: deaf1 c207y 2 dpf rep9; Danio rerio; RNA Seq	GSM8020164 r1	GSM8020164	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-wt_A10_S10_R1_001.fastq.gz	fastq	5417478400.0	53638400.0	GSM8020164 r1	0:101	A:1459560082;C:1269220844;G:1235271759;T:1453256921;N:168794	101	1459560082	1269220844	1235271759	1453256921	168794	SRX23261704	SRS20163669	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29952	29952	SRR27592977	SRX23261703	SRS20163668	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep8	GSM8020163	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y homozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y homozygous	GSM8020163	GSM8020163: deaf1 c207y 2 dpf rep8; Danio rerio; RNA Seq	GSM8020163 r1	GSM8020163	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-hom_A9_S9_R1_001.fastq.gz	fastq	2417886167.0	23939467.0	GSM8020163 r1	0:101	A:657342317;C:558713775;G:547590726;T:654164599;N:74750	101	657342317	558713775	547590726	654164599	74750	SRX23261703	SRS20163668	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29953	29953	SRR27592978	SRX23261702	SRS20163667	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep7	GSM8020162	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y homozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y homozygous	GSM8020162	GSM8020162: deaf1 c207y 2 dpf rep7; Danio rerio; RNA Seq	GSM8020162 r1	GSM8020162	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-hom_A8_S8_R1_001.fastq.gz	fastq	3601305288.0	35656488.0	GSM8020162 r1	0:101	A:974139857;C:839029639;G:822572729;T:965450738;N:112325	101	974139857	839029639	822572729	965450738	112325	SRX23261702	SRS20163667	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29954	29954	SRR27592979	SRX23261701	SRS20163666	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep6	GSM8020161	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y homozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y homozygous	GSM8020161	GSM8020161: deaf1 c207y 2 dpf rep6; Danio rerio; RNA Seq	GSM8020161 r1	GSM8020161	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-hom_A6_S6_R1_001.fastq.gz	fastq	2545549965.0	25203465.0	GSM8020161 r1	0:101	A:689302325;C:596907356;G:578571204;T:680690103;N:78977	101	689302325	596907356	578571204	680690103	78977	SRX23261701	SRS20163666	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29955	29955	SRR27592980	SRX23261700	SRS20163665	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep5	GSM8020160	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous	GSM8020160	GSM8020160: deaf1 c207y 2 dpf rep5; Danio rerio; RNA Seq	GSM8020160 r1	GSM8020160	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-het_A5_S5_R1_001.fastq.gz	fastq	3102857158.0	30721358.0	GSM8020160 r1	0:101	A:850838897;C:712670459;G:688515516;T:850736210;N:96076	101	850838897	712670459	688515516	850736210	96076	SRX23261700	SRS20163665	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29956	29956	SRR27592981	SRX23261699	SRS20163664	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep4	GSM8020159	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous	GSM8020159	GSM8020159: deaf1 c207y 2 dpf rep4; Danio rerio; RNA Seq	GSM8020159 r1	GSM8020159	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-het_A4_S4_R1_001.fastq.gz	fastq	3415651633.0	33818333.0	GSM8020159 r1	0:101	A:933225760;C:786732356;G:770845968;T:924742081;N:105468	101	933225760	786732356	770845968	924742081	105468	SRX23261699	SRS20163664	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29957	29957	SRR27592982	SRX23261698	SRS20163663	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep3	GSM8020158	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous	GSM8020158	GSM8020158: deaf1 c207y 2 dpf rep3; Danio rerio; RNA Seq	GSM8020158 r1	GSM8020158	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-het_A3_S3_R1_001.fastq.gz	fastq	3429734972.0	33957772.0	GSM8020158 r1	0:101	A:920850547;C:802940416;G:790735026;T:915103526;N:105457	101	920850547	802940416	790735026	915103526	105457	SRX23261698	SRS20163663	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29958	29958	SRR27592983	SRX23261697	SRS20163662	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep2	GSM8020157	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous	GSM8020157	GSM8020157: deaf1 c207y 2 dpf rep2; Danio rerio; RNA Seq	GSM8020157 r1	GSM8020157	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-het_A2_S2_R1_001.fastq.gz	fastq	2810870602.0	27830402.0	GSM8020157 r1	0:101	A:742011214;C:673773327;G:656344142;T:738655690;N:86229	101	742011214	673773327	656344142	738655690	86229	SRX23261697	SRS20163662	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29959	29959	SRR27592984	SRX23261696	SRS20163661	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 c207y 2 dpf rep1	GSM8020156	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous\|geo loc name:missing\|collection date:missing	deaf1 c207y 2 dpf rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 c207y heterozygous	GSM8020156	GSM8020156: deaf1 c207y 2 dpf rep1; Danio rerio; RNA Seq	GSM8020156 r1	GSM8020156	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-c207y-2dpf-het_A1_S1_R1_001.fastq.gz	fastq	4234517819.0	41925919.0	GSM8020156 r1	0:101	A:1104853000;C:1023572758;G:1001000314;T:1104961067;N:130680	101	1104853000	1023572758	1001000314	1104961067	130680	SRX23261696	SRS20163661	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Hatching	Embryo	Multi-tissue	Multi-system
29960	29960	SRR27592985	SRX23261695	SRS20163660	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep14	GSM8020155	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep14	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020155	GSM8020155: deaf1 6 dpf rep14; Danio rerio; RNA Seq	GSM8020155 r1	GSM8020155	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-wt_C4_S28_R1_001.fastq.gz	fastq	3929983225.0	38910725.0	GSM8020155 r1	0:101	A:1024547567;C:957640911;G:915138235;T:1032535260;N:121252	101	1024547567	957640911	915138235	1032535260	121252	SRX23261695	SRS20163660	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29961	29961	SRR27592986	SRX23261694	SRS20163658	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep13	GSM8020154	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep13	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020154	GSM8020154: deaf1 6 dpf rep13; Danio rerio; RNA Seq	GSM8020154 r1	GSM8020154	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-wt_C3_S27_R1_001.fastq.gz	fastq	3398044101.0	33644001.0	GSM8020154 r1	0:101	A:885187846;C:821364346;G:803770460;T:887617386;N:104063	101	885187846	821364346	803770460	887617386	104063	SRX23261694	SRS20163658	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29962	29962	SRR27592987	SRX23261693	SRS20163659	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep12	GSM8020153	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep12	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020153	GSM8020153: deaf1 6 dpf rep12; Danio rerio; RNA Seq	GSM8020153 r1	GSM8020153	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-wt_C2_S26_R1_001.fastq.gz	fastq	5035800713.0	49859413.0	GSM8020153 r1	0:101	A:1333647614;C:1193799648;G:1179125857;T:1329071614;N:155980	101	1333647614	1193799648	1179125857	1329071614	155980	SRX23261693	SRS20163659	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29963	29963	SRR27592988	SRX23261692	SRS20163657	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep11	GSM8020152	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i wild types	GSM8020152	GSM8020152: deaf1 6 dpf rep11; Danio rerio; RNA Seq	GSM8020152 r1	GSM8020152	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-wt_C1_S25_R1_001.fastq.gz	fastq	3565807727.0	35305027.0	GSM8020152 r1	0:101	A:912147405;C:880055335;G:858888661;T:914605631;N:110695	101	912147405	880055335	858888661	914605631	110695	SRX23261692	SRS20163657	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29964	29964	SRR27592989	SRX23261691	SRS20163655	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep10	GSM8020151	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020151	GSM8020151: deaf1 6 dpf rep10; Danio rerio; RNA Seq	GSM8020151 r1	GSM8020151	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-hom_B12_S24_R1_001.fastq.gz	fastq	3931681439.0	38927539.0	GSM8020151 r1	0:101	A:1019714387;C:963143457;G:926446608;T:1022254324;N:122663	101	1019714387	963143457	926446608	1022254324	122663	SRX23261691	SRS20163655	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29965	29965	SRR27592990	SRX23261690	SRS20163654	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep9	GSM8020150	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020150	GSM8020150: deaf1 6 dpf rep9; Danio rerio; RNA Seq	GSM8020150 r1	GSM8020150	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-hom_B11_S23_R1_001.fastq.gz	fastq	3494769074.0	34601674.0	GSM8020150 r1	0:101	A:900665381;C:855792466;G:834354551;T:903848341;N:108335	101	900665381	855792466	834354551	903848341	108335	SRX23261690	SRS20163654	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29966	29966	SRR27592991	SRX23261689	SRS20163653	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep8	GSM8020149	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020149	GSM8020149: deaf1 6 dpf rep8; Danio rerio; RNA Seq	GSM8020149 r1	GSM8020149	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-hom_B10_S22_R1_001.fastq.gz	fastq	5266326042.0	52141842.0	GSM8020149 r1	0:101	A:1377092992;C:1271335207;G:1235215906;T:1382519057;N:162880	101	1377092992	1271335207	1235215906	1382519057	162880	SRX23261689	SRS20163653	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29967	29967	SRR27592992	SRX23261688	SRS20163656	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep7	GSM8020148	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020148	GSM8020148: deaf1 6 dpf rep7; Danio rerio; RNA Seq	GSM8020148 r1	GSM8020148	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-hom_B9_S21_R1_001.fastq.gz	fastq	3981685832.0	39422632.0	GSM8020148 r1	0:101	A:1027397987;C:970696826;G:955899926;T:1027567681;N:123412	101	1027397987	970696826	955899926	1027567681	123412	SRX23261688	SRS20163656	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29968	29968	SRR27592993	SRX23261687	SRS20163652	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep6	GSM8020147	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i homozygous	GSM8020147	GSM8020147: deaf1 6 dpf rep6; Danio rerio; RNA Seq	GSM8020147 r1	GSM8020147	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-hom_B8_S20_R1_001.fastq.gz	fastq	3511062899.0	34762999.0	GSM8020147 r1	0:101	A:920619550;C:847444051;G:821952225;T:920937641;N:109432	101	920619550	847444051	821952225	920937641	109432	SRX23261687	SRS20163652	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29969	29969	SRR27592994	SRX23261686	SRS20163651	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep5	GSM8020146	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous	GSM8020146	GSM8020146: deaf1 6 dpf rep5; Danio rerio; RNA Seq	GSM8020146 r1	GSM8020146	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-het_B7_S19_R1_001.fastq.gz	fastq	3584512624.0	35490224.0	GSM8020146 r1	0:101	A:913282881;C:889075256;G:865104443;T:916938683;N:111361	101	913282881	889075256	865104443	916938683	111361	SRX23261686	SRS20163651	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29970	29970	SRR27592995	SRX23261685	SRS20163650	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		deaf1 6 dpf rep4	GSM8020145	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous\|geo loc name:missing\|collection date:missing	deaf1 6 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:deaf1 23d46i heterozygous	GSM8020145	GSM8020145: deaf1 6 dpf rep4; Danio rerio; RNA Seq	GSM8020145 r1	GSM8020145	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	deaf1-23d46i-6dpf-het_B6_S18_R1_001.fastq.gz	fastq	1942752978.0	19235178.0	GSM8020145 r1	0:101	A:510778300;C:474772116;G:456593849;T:500548378;N:60335	101	510778300	474772116	456593849	500548378	60335	SRX23261685	SRS20163650	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29972	29972	SRR27592997	SRX23261683	SRS20163648	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep11	GSM8020215	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b wild types\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep11	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b wild types	GSM8020215	GSM8020215: kmt5b 6 dpf rep11; Danio rerio; RNA Seq	GSM8020215 r1	GSM8020215	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-wt_ST12_S11_L001_R1_001.fastq.gz	fastq	2811106942.0	27832742.0	GSM8020215 r1	0:101	A:742607456;C:672481785;G:661003699;T:735010237;N:3765	101	742607456	672481785	661003699	735010237	3765	SRX23261683	SRS20163648	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29973	29973	SRR27592998	SRX23261682	SRS20163646	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep10	GSM8020214	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b wild types\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b wild types	GSM8020214	GSM8020214: kmt5b 6 dpf rep10; Danio rerio; RNA Seq	GSM8020214 r1	GSM8020214	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-wt_ST11_S10_L001_R1_001.fastq.gz	fastq	2995768474.0	29661074.0	GSM8020214 r1	0:101	A:778796313;C:726678609;G:718151791;T:772137908;N:3853	101	778796313	726678609	718151791	772137908	3853	SRX23261682	SRS20163646	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29974	29974	SRR27592999	SRX23261681	SRS20163647	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep9	GSM8020213	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b wild types\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b wild types	GSM8020213	GSM8020213: kmt5b 6 dpf rep9; Danio rerio; RNA Seq	GSM8020213 r1	GSM8020213	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-wt_ST10_S9_L001_R1_001.fastq.gz	fastq	3100692122.0	30699922.0	GSM8020213 r1	0:101	A:802618514;C:755714809;G:746538025;T:795816685;N:4089	101	802618514	755714809	746538025	795816685	4089	SRX23261681	SRS20163647	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29975	29975	SRR27593000	SRX23261680	SRS20163645	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep8	GSM8020212	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous	GSM8020212	GSM8020212: kmt5b 6 dpf rep8; Danio rerio; RNA Seq	GSM8020212 r1	GSM8020212	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-hom_ST9_S8_L001_R1_001.fastq.gz	fastq	3106011792.0	30752592.0	GSM8020212 r1	0:101	A:863424381;C:702180650;G:684425392;T:855977322;N:4047	101	863424381	702180650	684425392	855977322	4047	SRX23261680	SRS20163645	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29976	29976	SRR27593001	SRX23261679	SRS20163644	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep7	GSM8020211	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous	GSM8020211	GSM8020211: kmt5b 6 dpf rep7; Danio rerio; RNA Seq	GSM8020211 r1	GSM8020211	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-hom_ST8_S7_L001_R1_001.fastq.gz	fastq	3075023982.0	30445782.0	GSM8020211 r1	0:101	A:835646166;C:717541810;G:703459633;T:818372433;N:3940	101	835646166	717541810	703459633	818372433	3940	SRX23261679	SRS20163644	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29977	29977	SRR27593002	SRX23261678	SRS20163643	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep6	GSM8020210	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous	GSM8020210	GSM8020210: kmt5b 6 dpf rep6; Danio rerio; RNA Seq	GSM8020210 r1	GSM8020210	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-hom_ST7_S6_L001_R1_001.fastq.gz	fastq	2624342186.0	25983586.0	GSM8020210 r1	0:101	A:679347120;C:640703762;G:632252315;T:672035427;N:3562	101	679347120	640703762	632252315	672035427	3562	SRX23261678	SRS20163643	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29978	29978	SRR27593003	SRX23261677	SRS20163642	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep5	GSM8020209	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b homozygous	GSM8020209	GSM8020209: kmt5b 6 dpf rep5; Danio rerio; RNA Seq	GSM8020209 r1	GSM8020209	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-hom_ST6_S5_L001_R1_001.fastq.gz	fastq	5437715063.0	53838763.0	GSM8020209 r1	0:101	A:1481531392;C:1262906390;G:1249347683;T:1443922426;N:7172	101	1481531392	1262906390	1249347683	1443922426	7172	SRX23261677	SRS20163642	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29979	29979	SRR27593004	SRX23261676	SRS20163641	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep4	GSM8020208	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous	GSM8020208	GSM8020208: kmt5b 6 dpf rep4; Danio rerio; RNA Seq	GSM8020208 r1	GSM8020208	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-het_ST5_S4_L001_R1_001.fastq.gz	fastq	3496810587.0	34621887.0	GSM8020208 r1	0:101	A:920956592;C:840496211;G:832829579;T:902523782;N:4423	101	920956592	840496211	832829579	902523782	4423	SRX23261676	SRS20163641	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29980	29980	SRR27593005	SRX23261675	SRS20163640	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep3	GSM8020207	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous	GSM8020207	GSM8020207: kmt5b 6 dpf rep3; Danio rerio; RNA Seq	GSM8020207 r1	GSM8020207	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-het_ST4_S3_L001_R1_001.fastq.gz	fastq	3779380105.0	37419605.0	GSM8020207 r1	0:101	A:998848737;C:910675528;G:892963309;T:976887623;N:4908	101	998848737	910675528	892963309	976887623	4908	SRX23261675	SRS20163640	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29981	29981	SRR27593006	SRX23261674	SRS20163639	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep2	GSM8020206	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous	GSM8020206	GSM8020206: kmt5b 6 dpf rep2; Danio rerio; RNA Seq	GSM8020206 r1	GSM8020206	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-het_ST3_S2_L001_R1_001.fastq.gz	fastq	4697277599.0	46507699.0	GSM8020206 r1	0:101	A:1214157843;C:1147760212;G:1129537221;T:1205816178;N:6145	101	1214157843	1147760212	1129537221	1205816178	6145	SRX23261674	SRS20163639	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29982	29982	SRR27593007	SRX23261673	SRS20163638	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		kmt5b 6 dpf rep1	GSM8020205	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous\|geo loc name:missing\|collection date:missing	kmt5b 6 dpf rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:kmt5b heterozygous	GSM8020205	GSM8020205: kmt5b 6 dpf rep1; Danio rerio; RNA Seq	GSM8020205 r1	GSM8020205	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	kmt5b-6dpf-het_ST2_S1_L001_R1_001.fastq.gz	fastq	4057743175.0	40175675.0	GSM8020205 r1	0:101	A:1072507807;C:970584483;G:958817150;T:1055828545;N:5190	101	1072507807	970584483	958817150	1055828545	5190	SRX23261673	SRS20163638	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29983	29983	SRR27593008	SRX23261672	SRS20163637	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep10	GSM8020204	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep10	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types	GSM8020204	GSM8020204: hdlbpa 6 dpf rep10; Danio rerio; RNA Seq	GSM8020204 r1	GSM8020204	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-wt_H14_S21_L002_R1_001.fastq.gz	fastq	5345570642.0	52926442.0	GSM8020204 r1	0:101	A:1439943379;C:1249929878;G:1229033309;T:1426645468;N:18608	101	1439943379	1249929878	1229033309	1426645468	18608	SRX23261672	SRS20163637	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29984	29984	SRR27593009	SRX23261671	SRS20163636	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep9	GSM8020203	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep9	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types	GSM8020203	GSM8020203: hdlbpa 6 dpf rep9; Danio rerio; RNA Seq	GSM8020203 r1	GSM8020203	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-wt_H13_S20_L002_R1_001.fastq.gz	fastq	3927587101.0	38887001.0	GSM8020203 r1	0:101	A:1065676696;C:913744882;G:891757533;T:1056394325;N:13665	101	1065676696	913744882	891757533	1056394325	13665	SRX23261671	SRS20163636	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29985	29985	SRR27593010	SRX23261670	SRS20163635	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep8	GSM8020202	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep8	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types	GSM8020202	GSM8020202: hdlbpa 6 dpf rep8; Danio rerio; RNA Seq	GSM8020202 r1	GSM8020202	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-wt_H12_S19_L002_R1_001.fastq.gz	fastq	6495421706.0	64311106.0	GSM8020202 r1	0:101	A:1776534004;C:1513743907;G:1447648946;T:1757472399;N:22450	101	1776534004	1513743907	1447648946	1757472399	22450	SRX23261670	SRS20163635	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29986	29986	SRR27593011	SRX23261669	SRS20163634	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep7	GSM8020201	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep7	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa wild types	GSM8020201	GSM8020201: hdlbpa 6 dpf rep7; Danio rerio; RNA Seq	GSM8020201 r1	GSM8020201	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-wt_H11_S18_L002_R1_001.fastq.gz	fastq	3911576379.0	38728479.0	GSM8020201 r1	0:101	A:1058589544;C:907080870;G:898659386;T:1047232965;N:13614	101	1058589544	907080870	898659386	1047232965	13614	SRX23261669	SRS20163634	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29987	29987	SRR27593012	SRX23261668	SRS20163633	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep6	GSM8020200	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep6	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous	GSM8020200	GSM8020200: hdlbpa 6 dpf rep6; Danio rerio; RNA Seq	GSM8020200 r1	GSM8020200	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-hom_H9_S16_L002_R1_001.fastq.gz	fastq	1927080000.0	19080000.0	GSM8020200 r1	0:101	A:523643390;C:445913624;G:440889014;T:516627902;N:6070	101	523643390	445913624	440889014	516627902	6070	SRX23261668	SRS20163633	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29988	29988	SRR27593013	SRX23261667	SRS20163632	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep5	GSM8020199	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep5	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous	GSM8020199	GSM8020199: hdlbpa 6 dpf rep5; Danio rerio; RNA Seq	GSM8020199 r1	GSM8020199	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-hom_H8_S15_L002_R1_001.fastq.gz	fastq	1946049618.0	19267818.0	GSM8020199 r1	0:101	A:539909954;C:443888173;G:429627730;T:532616963;N:6798	101	539909954	443888173	429627730	532616963	6798	SRX23261667	SRS20163632	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29989	29989	SRR27593014	SRX23261666	SRS20163631	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep4	GSM8020198	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep4	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous	GSM8020198	GSM8020198: hdlbpa 6 dpf rep4; Danio rerio; RNA Seq	GSM8020198 r1	GSM8020198	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-hom_H7_S14_L002_R1_001.fastq.gz	fastq	1039274749.0	10289849.0	GSM8020198 r1	0:101	A:283894686;C:241034413;G:233108651;T:281233307;N:3692	101	283894686	241034413	233108651	281233307	3692	SRX23261666	SRS20163631	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29990	29990	SRR27593015	SRX23261665	SRS20163630	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep3	GSM8020197	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep3	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa homozygous	GSM8020197	GSM8020197: hdlbpa 6 dpf rep3; Danio rerio; RNA Seq	GSM8020197 r1	GSM8020197	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-hom_H10_S17_L002_R1_001.fastq.gz	fastq	4044191399.0	40041499.0	GSM8020197 r1	0:101	A:1104383207;C:936931840;G:907616152;T:1095246283;N:13917	101	1104383207	936931840	907616152	1095246283	13917	SRX23261665	SRS20163630	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29991	29991	SRR27593016	SRX23261664	SRS20163629	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep2	GSM8020196	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa heterozygous\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep2	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa heterozygous	GSM8020196	GSM8020196: hdlbpa 6 dpf rep2; Danio rerio; RNA Seq	GSM8020196 r1	GSM8020196	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-het_H5_S13_L002_R1_001.fastq.gz	fastq	1470627771.0	14560671.0	GSM8020196 r1	0:101	A:405621136;C:336868389;G:326203713;T:401929517;N:5016	101	405621136	336868389	326203713	401929517	5016	SRX23261664	SRS20163629	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-system
29992	29992	SRR27593017	SRX23261663	SRS20163628	SRP484215	PRJNA1065838	Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations	GSE253405	Transcriptome Analysis	Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.		hdlbpa 6 dpf rep1	GSM8020195	source name:head with eyes 2 5 heads combined\|tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa heterozygous\|geo loc name:missing\|collection date:missing	hdlbpa 6 dpf rep1	Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.	head with eyes 2 5 heads combined	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	tissue:head with eyes 2 5 heads combined\|genotype:hdlbpa heterozygous	GSM8020195	GSM8020195: hdlbpa 6 dpf rep1; Danio rerio; RNA Seq	GSM8020195 r1	GSM8020195	1	RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484215	loader:fastq load.py	hdlbpa-6dpf-het_H3_S12_L002_R1_001.fastq.gz	fastq	1550552101.0	15352001.0	GSM8020195 r1	0:101	A:410548977;C:370146379;G:359721543;T:410129702;N:5500	101	410548977	370146379	359721543	410129702	5500	SRX23261663	SRS20163628	SRA1787174	UMass Chan Medical School	UMass Chan Medical School							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2024-01-16	Larval	Larval	Multi-tissue	Multi-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");;