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
175,DRR084197,DRX078028,DRS086522,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],SAMD00073604,,sample name:M 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073604,DRX078028,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073604,,,,1389837888.0,38606608.0,DRR084197,0:36,A:320671418;C:336948866;G:347550258;T:381720581;N:2946765,36,,,,320671418,336948866,347550258,381720581,2946765,DRX078028,DRS086522,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89763,,0.02235,,0.76445,,0.46381,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
181,DRR084191,DRX078022,DRS086516,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],SAMD00073598,,sample name:M|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073598,DRX078022,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,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>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073598,,,,1050981012.0,29193917.0,DRR084191,0:36,A:241048832;C:256186268;G:260277071;T:293299597;N:169244,36,,,,241048832,256186268,260277071,293299597,169244,DRX078022,DRS086516,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.9088,,0.02369,,0.7624,,0.47998,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
9812,ERR3931362,ERX3938952,ERS4329529,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 7 ED,SAMEA6565186,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565186|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 ED,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 7 ED s,WKM 7 ED s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,10_WKM_7_ED.fastq.gz,fastq,3603783627.0,47724788.0,E MTAB 8800:WKM 7 ED,0:75.51 1:0,A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509,75,0,,,730277817,1059558661,1006087781,807771859,87509,ERX3938952,ERS4329529,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96114,,0.20335,,0.83798,,0.76524,,76,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9813,ERR3931361,ERX3938951,ERS4329528,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 7 EaD,SAMEA6565185,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565185|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 EaD,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 7 EaD s,WKM 7 EaD s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:kit ligand,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,11_WKM_7_EaD_1.fastq.gz,fastq,3127207407.0,41417754.0,E MTAB 8800:WKM 7 EaD,0:75.50 1:0,A:618290483;C:948661192;G:891134088;T:669046822;N:74822,75,0,,,618290483,948661192,891134088,669046822,74822,ERX3938951,ERS4329528,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96441,,0.20171,,0.85427,,0.75425,,76,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9814,ERR3931360,ERX3938950,ERS4329527,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 5 ED,SAMEA6565184,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565184|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 ED,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 5 ED s,WKM 5 ED s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,8_WKM_5_ED.fastq.gz,fastq,3762435507.0,49825705.0,E MTAB 8800:WKM 5 ED,0:75.51 1:0,A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573,75,0,,,760573477,1107794761,1060998015,832975681,93573,ERX3938950,ERS4329527,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96233,,0.20628,,0.84141,,0.73601,,75,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9815,ERR3931359,ERX3938949,ERS4329526,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 5 EaD,SAMEA6565183,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 5 EaD s,WKM 5 EaD s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:kit ligand,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,9_WKM_5_EaD.fastq.gz,fastq,3602342027.0,47707938.0,E MTAB 8800:WKM 5 EaD,0:75.51 1:0,A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286,75,0,,,717278291,1084375347,1027250408,773351695,86286,ERX3938949,ERS4329526,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96461,,0.20281,,0.85303,,0.74553,,75,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
10186,ERR6212423,ERX5847531,ERS7094943,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Naive,SAMEA9361876,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Naive p,Naive p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz,fastq fastq fastq,60168324125.0,481346593.0,E MTAB 10379 3:Naive,0:8 1:27 2:90,A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241,8,27,90,,12424400694,9366563781,10029312355,11497237299,3679241,ERX5847531,ERS7094943,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.94834,,0.09482,,0.802,,0.5277,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10187,ERR6212422,ERX5847530,ERS7094942,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Lesi1d,SAMEA9361875,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Lesioned p,Lesioned p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:spinal cord lesion,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz,fastq fastq fastq,61701873000.0,493614984.0,E MTAB 10379 3:Lesioned,0:8 1:27 2:90,A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277,8,27,90,,12952533019,9222397450,9920185920,12326470894,3761277,ERX5847530,ERS7094942,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.93082,,0.10862,,0.80302,,0.54924,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
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