rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
51,DRR029943,DRX026961,DRS086501,DRP004756,PRJDB3475,Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004756,Other,To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.,,,oocyte maturation duirng natural paring,zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq],SAMD00025433,,sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00025433,DRX026961,5 OM,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004756,Illumina HiSeq 2500 sequencing of SAMD00025433,,,,573617016.0,15933806.0,DRR029943,0:36,A:130606804;C:141376330;G:145891720;T:155734276;N:7886,36,,,,130606804,141376330,145891720,155734276,7886,DRX026961,DRS086501,DRA003031,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91108,,0.0173,,0.76205,,0.46319,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Multi-tissue,Multi-system
168,DRR075402,DRX069316,DRS075497,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The liver of tumor fish 7dpf,Tumor liver,SAMD00065416,,sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065416,DRX069316,Tumor liver,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065416,,,,1091167236.0,30310201.0,DRR075402,0:36,A:272216839;C:257523620;G:259746158;T:301642763;N:37856,36,,,,272216839,257523620,259746158,301642763,37856,DRX069316,DRS075497,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.90443,,0.08935,,0.71863,,0.51145,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
169,DRR075401,DRX069315,DRS075496,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The gut of tumor fish 7dpf,Tumor gut,SAMD00065415,,sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065415,DRX069315,Tumor gut,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065415,,,,1423792872.0,39549802.0,DRR075401,0:36,A:342328685;C:346616167;G:341519547;T:393278536;N:49937,36,,,,342328685,346616167,341519547,393278536,49937,DRX069315,DRS075496,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.91303,,0.0869,,0.70494,,0.44332,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
170,DRR075400,DRX069314,DRS075495,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The remaining part of body of tumor fish 7dpf,Tumor body,SAMD00065414,,sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065414,DRX069314,Tumor body,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065414,,,,1168514964.0,32458749.0,DRR075400,0:36,A:286579925;C:275496498;G:278133055;T:328265078;N:40408,36,,,,286579925,275496498,278133055,328265078,40408,DRX069314,DRS075495,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.89927,,0.15051,,0.66714,,0.47579,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Multi-tissue,Multi-system
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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