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
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
10147,ERR5005147,ERX4814430,ERS5474667,ERP125923,PRJEB42059,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E-MTAB-9924,Other,DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,,Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,6wpf rep2 RNA,SAMEA7727294,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,",ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727294|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep2 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen,,,,,,,,,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E MTAB 9924:6wpf rep2 RNA p,6wpf rep2 RNA p,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,HiSeq X Ten,,ERP125923,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,6wpf_rep2_RNA_R1.fastq.gz 6wpf_rep2_RNA_R2.fastq.gz,fastq fastq,11929324428.0,40157012.0,E MTAB 9924:6wpf rep2 RNA R,0:148.72 1:148.34,A:3237937670;C:2713313024;G:2724528618;T:3251908184;N:1636932,148,148,,,3237937670,2713313024,2724528618,3251908184,1636932,ERX4814430,ERS5474667,ERA3199751,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive","Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive",2,0.93069,0.93326,0.13891,0.13708,0.69779,0.71701,0.49797,0.49993,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2020-12-17,Larval,Larval,Multi-tissue,Multi-system
10148,ERR5005146,ERX4814429,ERS5474666,ERP125923,PRJEB42059,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E-MTAB-9924,Other,DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,,Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,6wpf rep1 RNA,SAMEA7727293,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,",ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727293|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep1 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen,,,,,,,,,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E MTAB 9924:6wpf rep1 RNA p,6wpf rep1 RNA p,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,HiSeq X Ten,,ERP125923,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,6wpf_rep1_RNA_R1.fastq.gz 6wpf_rep1_RNA_R2.fastq.gz,fastq fastq,19633084666.0,66362913.0,E MTAB 9924:6wpf rep1 RNA R,0:148.10 1:147.74,A:5348913370;C:4443593237;G:4456508875;T:5380825384;N:3243800,148,147,,,5348913370,4443593237,4456508875,5380825384,3243800,ERX4814429,ERS5474666,ERA3199751,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive","Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive",2,0.92182,0.92338,0.12138,0.11866,0.68499,0.70236,0.50638,0.51742,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2020-12-17,Larval,Larval,Multi-tissue,Multi-system
10151,ERR5005143,ERX4814426,ERS5474663,ERP125923,PRJEB42059,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E-MTAB-9924,Other,DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,,Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,4wpf rep2 RNA,SAMEA7727290,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,",ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727290|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:4wpf rep2 RNA|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:4wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen,,,,,,,,,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E MTAB 9924:4wpf rep2 RNA p,4wpf rep2 RNA p,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,Experimental Factor: age:4|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,HiSeq X Ten,,ERP125923,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,4wpf_rep2_RNA_R1.fastq.gz 4wpf_rep2_RNA_R2.fastq.gz,fastq fastq,17862998816.0,62733750.0,E MTAB 9924:4wpf rep2 RNA R,0:142.46 1:142.28,A:4963776868;C:3947656384;G:3887833339;T:5057912943;N:5819282,142,142,,,4963776868,3947656384,3887833339,5057912943,5819282,ERX4814426,ERS5474663,ERA3199751,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive","Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive",2,0.9309,0.93111,0.1952,0.1951,0.70534,0.7176,0.50482,0.51152,116,147,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2020-12-17,Larval,Larval,Multi-tissue,Multi-system
10152,ERR5005142,ERX4814425,ERS5474662,ERP125923,PRJEB42059,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E-MTAB-9924,Other,DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,,Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,4wpf rep1 RNA,SAMEA7727289,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,",ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727289|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:4wpf rep1 RNA|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:4wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen,,,,,,,,,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E MTAB 9924:4wpf rep1 RNA p,4wpf rep1 RNA p,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,Experimental Factor: age:4|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,HiSeq X Ten,,ERP125923,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,4wpf_rep1_RNA_R1.fastq.gz 4wpf_rep1_RNA_R2.fastq.gz,fastq fastq,17991275539.0,62100394.0,E MTAB 9924:4wpf rep1 RNA R,0:144.97 1:144.75,A:5021314085;C:3954412393;G:3881029269;T:5128240171;N:6279621,144,144,,,5021314085,3954412393,3881029269,5128240171,6279621,ERX4814425,ERS5474662,ERA3199751,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive","Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive",2,0.92732,0.92708,0.18879,0.18795,0.70171,0.71634,0.506,0.50887,150,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2020-12-17,Larval,Larval,Multi-tissue,Multi-system
10153,ERR5005141,ERX4814424,ERS5474661,ERP125923,PRJEB42059,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E-MTAB-9924,Other,DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,,Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,3wpf rep2 RNA,SAMEA7727288,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,",ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727288|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep2 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen,,,,,,,,,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E MTAB 9924:3wpf rep2 RNA p,3wpf rep2 RNA p,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,HiSeq X Ten,,ERP125923,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,3wpf_rep2_RNA_R1.fastq.gz 3wpf_rep2_RNA_R2.fastq.gz,fastq fastq,22804042203.0,76957632.0,E MTAB 9924:3wpf rep2 RNA R,0:148.34 1:147.98,A:6255991654;C:5120232312;G:5136799470;T:6288581486;N:2437281,148,147,,,6255991654,5120232312,5136799470,6288581486,2437281,ERX4814424,ERS5474661,ERA3199751,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive","Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive",2,0.93211,0.93322,0.20907,0.2056,0.6983,0.71652,0.53448,0.5352,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2020-12-17,Larval,Larval,Multi-tissue,Multi-system
10154,ERR5005140,ERX4814423,ERS5474660,ERP125923,PRJEB42059,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E-MTAB-9924,Other,DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,,Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,3wpf rep1 RNA,SAMEA7727287,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,",ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727287|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep1 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen,,,,,,,,,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,E MTAB 9924:3wpf rep1 RNA p,3wpf rep1 RNA p,RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.,Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,HiSeq X Ten,,ERP125923,HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain,ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17,3wpf_rep1_RNA_R1.fastq.gz 3wpf_rep1_RNA_R2.fastq.gz,fastq fastq,25549987003.0,86260528.0,E MTAB 9924:3wpf rep1 RNA R,0:148.28 1:147.91,A:6961927451;C:5786809647;G:5798882444;T:6999483818;N:2883643,148,147,,,6961927451,5786809647,5798882444,6999483818,2883643,ERX4814423,ERS5474660,ERA3199751,"Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive","Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive",2,0.93267,0.93467,0.20372,0.20263,0.69252,0.70962,0.53426,0.54087,149,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2020-12-17,Larval,Larval,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
25237,SRR25721801,SRX21445937,SRS18680715,SRP456253,PRJNA1007646,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva],GSE241296,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 µm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 µl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 µl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 µm opening. The solution was filtered through a 35 µm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing,,,,zebrafish larva  neurons and glia  scRNAseq,GSM7720759,,source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing,zebrafish larva  neurons and glia  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish larva,,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf,GSM7720759,GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq,GSM7720759 r1,GSM7720759,1,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456253,,loader:fastq load.py,CEL210928PB_HW1008_SAIG_D7_S1_L002_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,55936355640.0,254256162.0,GSM7720759 r1,0:10 1:10 2:100 3:100,A:13207297968;C:10496996981;G:10989402500;T:16156355819;N:1179132,10,10,100,100,13207297968,10496996981,10989402500,16156355819,1179132,SRX21445937,SRS18680715,SRA1696793,Oregon Health and Science Univ,Oregon Health and Science Univ,2,0.0,0.81961,0.0,0.19165,1.0,0.8508,,0.59575,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-21,Larval,Larval,Multi-tissue,Multi-system
25238,SRR25721802,SRX21445937,SRS18680715,SRP456253,PRJNA1007646,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva],GSE241296,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 µm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 µl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 µl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 µm opening. The solution was filtered through a 35 µm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing,,,,zebrafish larva  neurons and glia  scRNAseq,GSM7720759,,source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing,zebrafish larva  neurons and glia  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish larva,,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf,GSM7720759,GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq,GSM7720759 r1,GSM7720759,1,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456253,,loader:fastq load.py,CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,54474841080.0,247612914.0,GSM7720759 r2,0:10 1:10 2:100 3:100,A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834,10,10,100,100,12887048507,10210716068,10683375130,15740176261,1266834,SRX21445937,SRS18680715,SRA1696793,Oregon Health and Science Univ,Oregon Health and Science Univ,2,0.0,0.82189,0.0,0.19349,1.0,0.85025,,0.6092,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-21,Larval,Larval,Multi-tissue,Multi-system
26518,SRR26050763,SRX21767119,SRS18873424,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells,GSM7778660,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ,GSM7778660,GSM7778660: psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778660 r1,GSM7778660,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_M4_R1_001.fastq.gz sox10_M4_R2_001.fastq.gz,fastq fastq,17203316400.0,57344388.0,GSM7778660 r1,0:150 1:150,A:4557769784;C:4038080087;G:4028545423;T:4578857383;N:63723,150,150,,,4557769784,4038080087,4028545423,4578857383,63723,SRX21767119,SRS18873424,SRA1711572,BWH,BWH,2,0.93924,0.93866,0.10703,0.1068,0.70597,0.70508,0.52195,0.52023,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26519,SRR26050764,SRX21767118,SRS18873423,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells,GSM7778659,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ,GSM7778659,GSM7778659: psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778659 r1,GSM7778659,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_M3_R1_001.fastq.gz sox10_M3_R2_001.fastq.gz,fastq fastq,16490564400.0,54968548.0,GSM7778659 r1,0:150 1:150,A:4465032867;C:3767540674;G:3755500192;T:4502428180;N:62487,150,150,,,4465032867,3767540674,3755500192,4502428180,62487,SRX21767118,SRS18873423,SRA1711572,BWH,BWH,2,0.92805,0.92792,0.14244,0.14225,0.69639,0.69757,0.52133,0.52056,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26520,SRR26050765,SRX21767117,SRS18873422,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells,GSM7778658,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ,GSM7778658,GSM7778658: psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778658 r1,GSM7778658,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_M1_R1_001.fastq.gz sox10_M1_R2_001.fastq.gz,fastq fastq,14363136600.0,47877122.0,GSM7778658 r1,0:150 1:150,A:3843987690;C:3329370255;G:3310959116;T:3878765025;N:54514,150,150,,,3843987690,3329370255,3310959116,3878765025,54514,SRX21767117,SRS18873422,SRA1711572,BWH,BWH,2,0.92722,0.92625,0.11695,0.11644,0.69611,0.6969,0.52036,0.522,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26521,SRR26050766,SRX21767116,SRS18873421,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells,GSM7778657,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778657,GSM7778657: psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778657 r1,GSM7778657,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH4_R1_001.fastq.gz sox10_WH4_R2_001.fastq.gz,fastq fastq,14383303200.0,47944344.0,GSM7778657 r1,0:150 1:150,A:3825787510;C:3356860561;G:3322388892;T:3878211922;N:54315,150,150,,,3825787510,3356860561,3322388892,3878211922,54315,SRX21767116,SRS18873421,SRA1711572,BWH,BWH,2,0.93157,0.93024,0.09771,0.09735,0.7177,0.71829,0.52664,0.52877,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26522,SRR26050767,SRX21767115,SRS18873420,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells,GSM7778656,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778656,GSM7778656: psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778656 r1,GSM7778656,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH3_R1_001.fastq.gz sox10_WH3_R2_001.fastq.gz,fastq fastq,13772364600.0,45907882.0,GSM7778656 r1,0:150 1:150,A:3599468762;C:3277366623;G:3241941715;T:3653534992;N:52508,150,150,,,3599468762,3277366623,3241941715,3653534992,52508,SRX21767115,SRS18873420,SRA1711572,BWH,BWH,2,0.94023,0.93961,0.07684,0.07628,0.70654,0.70682,0.50963,0.51111,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26523,SRR26050768,SRX21767114,SRS18873419,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells,GSM7778655,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778655,GSM7778655: psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778655 r1,GSM7778655,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH2_R1_001.fastq.gz sox10_WH2_R2_001.fastq.gz,fastq fastq,15229813200.0,50766044.0,GSM7778655 r1,0:150 1:150,A:4029459993;C:3570808650;G:3534029380;T:4095461104;N:54073,150,150,,,4029459993,3570808650,3534029380,4095461104,54073,SRX21767114,SRS18873419,SRA1711572,BWH,BWH,2,0.93346,0.93269,0.13006,0.13022,0.70094,0.70007,0.51067,0.50945,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26524,SRR26050769,SRX21767113,SRS18873418,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells,GSM7778654,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778654,GSM7778654: psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778654 r1,GSM7778654,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH1_R1_001.fastq.gz sox10_WH1_R2_001.fastq.gz,fastq fastq,13483692600.0,44945642.0,GSM7778654 r1,0:150 1:150,A:3567731759;C:3163438678;G:3137216449;T:3615254758;N:50956,150,150,,,3567731759,3163438678,3137216449,3615254758,50956,SRX21767113,SRS18873418,SRA1711572,BWH,BWH,2,0.92459,0.92408,0.11911,0.11956,0.7027,0.70264,0.50884,0.50322,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,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
29960,SRR27592985,SRX23261695,SRS20163660,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep14,GSM8020155,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep14,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types,GSM8020155,GSM8020155: deaf1  6 dpf  rep14; Danio rerio; RNA Seq,GSM8020155 r1,GSM8020155,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-wt_C4_S28_R1_001.fastq.gz,fastq,3929983225.0,38910725.0,GSM8020155 r1,0:101,A:1024547567;C:957640911;G:915138235;T:1032535260;N:121252,101,,,,1024547567,957640911,915138235,1032535260,121252,SRX23261695,SRS20163660,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29961,SRR27592986,SRX23261694,SRS20163658,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep13,GSM8020154,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep13,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types,GSM8020154,GSM8020154: deaf1  6 dpf  rep13; Danio rerio; RNA Seq,GSM8020154 r1,GSM8020154,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-wt_C3_S27_R1_001.fastq.gz,fastq,3398044101.0,33644001.0,GSM8020154 r1,0:101,A:885187846;C:821364346;G:803770460;T:887617386;N:104063,101,,,,885187846,821364346,803770460,887617386,104063,SRX23261694,SRS20163658,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29962,SRR27592987,SRX23261693,SRS20163659,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep12,GSM8020153,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep12,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types,GSM8020153,GSM8020153: deaf1  6 dpf  rep12; Danio rerio; RNA Seq,GSM8020153 r1,GSM8020153,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-wt_C2_S26_R1_001.fastq.gz,fastq,5035800713.0,49859413.0,GSM8020153 r1,0:101,A:1333647614;C:1193799648;G:1179125857;T:1329071614;N:155980,101,,,,1333647614,1193799648,1179125857,1329071614,155980,SRX23261693,SRS20163659,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29963,SRR27592988,SRX23261692,SRS20163657,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep11,GSM8020152,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep11,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types,GSM8020152,GSM8020152: deaf1  6 dpf  rep11; Danio rerio; RNA Seq,GSM8020152 r1,GSM8020152,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-wt_C1_S25_R1_001.fastq.gz,fastq,3565807727.0,35305027.0,GSM8020152 r1,0:101,A:912147405;C:880055335;G:858888661;T:914605631;N:110695,101,,,,912147405,880055335,858888661,914605631,110695,SRX23261692,SRS20163657,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29964,SRR27592989,SRX23261691,SRS20163655,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep10,GSM8020151,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep10,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous,GSM8020151,GSM8020151: deaf1  6 dpf  rep10; Danio rerio; RNA Seq,GSM8020151 r1,GSM8020151,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-hom_B12_S24_R1_001.fastq.gz,fastq,3931681439.0,38927539.0,GSM8020151 r1,0:101,A:1019714387;C:963143457;G:926446608;T:1022254324;N:122663,101,,,,1019714387,963143457,926446608,1022254324,122663,SRX23261691,SRS20163655,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29965,SRR27592990,SRX23261690,SRS20163654,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep9,GSM8020150,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep9,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous,GSM8020150,GSM8020150: deaf1  6 dpf  rep9; Danio rerio; RNA Seq,GSM8020150 r1,GSM8020150,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-hom_B11_S23_R1_001.fastq.gz,fastq,3494769074.0,34601674.0,GSM8020150 r1,0:101,A:900665381;C:855792466;G:834354551;T:903848341;N:108335,101,,,,900665381,855792466,834354551,903848341,108335,SRX23261690,SRS20163654,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29966,SRR27592991,SRX23261689,SRS20163653,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep8,GSM8020149,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep8,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous,GSM8020149,GSM8020149: deaf1  6 dpf  rep8; Danio rerio; RNA Seq,GSM8020149 r1,GSM8020149,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-hom_B10_S22_R1_001.fastq.gz,fastq,5266326042.0,52141842.0,GSM8020149 r1,0:101,A:1377092992;C:1271335207;G:1235215906;T:1382519057;N:162880,101,,,,1377092992,1271335207,1235215906,1382519057,162880,SRX23261689,SRS20163653,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29967,SRR27592992,SRX23261688,SRS20163656,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep7,GSM8020148,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep7,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous,GSM8020148,GSM8020148: deaf1  6 dpf  rep7; Danio rerio; RNA Seq,GSM8020148 r1,GSM8020148,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-hom_B9_S21_R1_001.fastq.gz,fastq,3981685832.0,39422632.0,GSM8020148 r1,0:101,A:1027397987;C:970696826;G:955899926;T:1027567681;N:123412,101,,,,1027397987,970696826,955899926,1027567681,123412,SRX23261688,SRS20163656,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29968,SRR27592993,SRX23261687,SRS20163652,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep6,GSM8020147,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep6,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous,GSM8020147,GSM8020147: deaf1  6 dpf  rep6; Danio rerio; RNA Seq,GSM8020147 r1,GSM8020147,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-hom_B8_S20_R1_001.fastq.gz,fastq,3511062899.0,34762999.0,GSM8020147 r1,0:101,A:920619550;C:847444051;G:821952225;T:920937641;N:109432,101,,,,920619550,847444051,821952225,920937641,109432,SRX23261687,SRS20163652,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29969,SRR27592994,SRX23261686,SRS20163651,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep5,GSM8020146,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep5,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous,GSM8020146,GSM8020146: deaf1  6 dpf  rep5; Danio rerio; RNA Seq,GSM8020146 r1,GSM8020146,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-het_B7_S19_R1_001.fastq.gz,fastq,3584512624.0,35490224.0,GSM8020146 r1,0:101,A:913282881;C:889075256;G:865104443;T:916938683;N:111361,101,,,,913282881,889075256,865104443,916938683,111361,SRX23261686,SRS20163651,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29970,SRR27592995,SRX23261685,SRS20163650,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,deaf1  6 dpf  rep4,GSM8020145,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing,deaf1  6 dpf  rep4,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous,GSM8020145,GSM8020145: deaf1  6 dpf  rep4; Danio rerio; RNA Seq,GSM8020145 r1,GSM8020145,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,deaf1-23d46i-6dpf-het_B6_S18_R1_001.fastq.gz,fastq,1942752978.0,19235178.0,GSM8020145 r1,0:101,A:510778300;C:474772116;G:456593849;T:500548378;N:60335,101,,,,510778300,474772116,456593849,500548378,60335,SRX23261685,SRS20163650,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29972,SRR27592997,SRX23261683,SRS20163648,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep11,GSM8020215,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b wild types|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep11,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b wild types,GSM8020215,GSM8020215: kmt5b  6 dpf  rep11; Danio rerio; RNA Seq,GSM8020215 r1,GSM8020215,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-wt_ST12_S11_L001_R1_001.fastq.gz,fastq,2811106942.0,27832742.0,GSM8020215 r1,0:101,A:742607456;C:672481785;G:661003699;T:735010237;N:3765,101,,,,742607456,672481785,661003699,735010237,3765,SRX23261683,SRS20163648,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29973,SRR27592998,SRX23261682,SRS20163646,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep10,GSM8020214,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b wild types|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep10,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b wild types,GSM8020214,GSM8020214: kmt5b  6 dpf  rep10; Danio rerio; RNA Seq,GSM8020214 r1,GSM8020214,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-wt_ST11_S10_L001_R1_001.fastq.gz,fastq,2995768474.0,29661074.0,GSM8020214 r1,0:101,A:778796313;C:726678609;G:718151791;T:772137908;N:3853,101,,,,778796313,726678609,718151791,772137908,3853,SRX23261682,SRS20163646,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29974,SRR27592999,SRX23261681,SRS20163647,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep9,GSM8020213,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b wild types|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep9,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b wild types,GSM8020213,GSM8020213: kmt5b  6 dpf  rep9; Danio rerio; RNA Seq,GSM8020213 r1,GSM8020213,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-wt_ST10_S9_L001_R1_001.fastq.gz,fastq,3100692122.0,30699922.0,GSM8020213 r1,0:101,A:802618514;C:755714809;G:746538025;T:795816685;N:4089,101,,,,802618514,755714809,746538025,795816685,4089,SRX23261681,SRS20163647,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29975,SRR27593000,SRX23261680,SRS20163645,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep8,GSM8020212,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep8,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous,GSM8020212,GSM8020212: kmt5b  6 dpf  rep8; Danio rerio; RNA Seq,GSM8020212 r1,GSM8020212,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-hom_ST9_S8_L001_R1_001.fastq.gz,fastq,3106011792.0,30752592.0,GSM8020212 r1,0:101,A:863424381;C:702180650;G:684425392;T:855977322;N:4047,101,,,,863424381,702180650,684425392,855977322,4047,SRX23261680,SRS20163645,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29976,SRR27593001,SRX23261679,SRS20163644,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep7,GSM8020211,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep7,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous,GSM8020211,GSM8020211: kmt5b  6 dpf  rep7; Danio rerio; RNA Seq,GSM8020211 r1,GSM8020211,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-hom_ST8_S7_L001_R1_001.fastq.gz,fastq,3075023982.0,30445782.0,GSM8020211 r1,0:101,A:835646166;C:717541810;G:703459633;T:818372433;N:3940,101,,,,835646166,717541810,703459633,818372433,3940,SRX23261679,SRS20163644,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29977,SRR27593002,SRX23261678,SRS20163643,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep6,GSM8020210,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep6,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous,GSM8020210,GSM8020210: kmt5b  6 dpf  rep6; Danio rerio; RNA Seq,GSM8020210 r1,GSM8020210,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-hom_ST7_S6_L001_R1_001.fastq.gz,fastq,2624342186.0,25983586.0,GSM8020210 r1,0:101,A:679347120;C:640703762;G:632252315;T:672035427;N:3562,101,,,,679347120,640703762,632252315,672035427,3562,SRX23261678,SRS20163643,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29978,SRR27593003,SRX23261677,SRS20163642,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep5,GSM8020209,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep5,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b homozygous,GSM8020209,GSM8020209: kmt5b  6 dpf  rep5; Danio rerio; RNA Seq,GSM8020209 r1,GSM8020209,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-hom_ST6_S5_L001_R1_001.fastq.gz,fastq,5437715063.0,53838763.0,GSM8020209 r1,0:101,A:1481531392;C:1262906390;G:1249347683;T:1443922426;N:7172,101,,,,1481531392,1262906390,1249347683,1443922426,7172,SRX23261677,SRS20163642,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29979,SRR27593004,SRX23261676,SRS20163641,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep4,GSM8020208,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep4,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous,GSM8020208,GSM8020208: kmt5b  6 dpf  rep4; Danio rerio; RNA Seq,GSM8020208 r1,GSM8020208,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-het_ST5_S4_L001_R1_001.fastq.gz,fastq,3496810587.0,34621887.0,GSM8020208 r1,0:101,A:920956592;C:840496211;G:832829579;T:902523782;N:4423,101,,,,920956592,840496211,832829579,902523782,4423,SRX23261676,SRS20163641,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29980,SRR27593005,SRX23261675,SRS20163640,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep3,GSM8020207,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep3,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous,GSM8020207,GSM8020207: kmt5b  6 dpf  rep3; Danio rerio; RNA Seq,GSM8020207 r1,GSM8020207,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-het_ST4_S3_L001_R1_001.fastq.gz,fastq,3779380105.0,37419605.0,GSM8020207 r1,0:101,A:998848737;C:910675528;G:892963309;T:976887623;N:4908,101,,,,998848737,910675528,892963309,976887623,4908,SRX23261675,SRS20163640,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29981,SRR27593006,SRX23261674,SRS20163639,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep2,GSM8020206,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep2,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous,GSM8020206,GSM8020206: kmt5b  6 dpf  rep2; Danio rerio; RNA Seq,GSM8020206 r1,GSM8020206,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-het_ST3_S2_L001_R1_001.fastq.gz,fastq,4697277599.0,46507699.0,GSM8020206 r1,0:101,A:1214157843;C:1147760212;G:1129537221;T:1205816178;N:6145,101,,,,1214157843,1147760212,1129537221,1205816178,6145,SRX23261674,SRS20163639,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29982,SRR27593007,SRX23261673,SRS20163638,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,kmt5b  6 dpf  rep1,GSM8020205,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous|geo loc name:missing|collection date:missing,kmt5b  6 dpf  rep1,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:kmt5b heterozygous,GSM8020205,GSM8020205: kmt5b  6 dpf  rep1; Danio rerio; RNA Seq,GSM8020205 r1,GSM8020205,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,kmt5b-6dpf-het_ST2_S1_L001_R1_001.fastq.gz,fastq,4057743175.0,40175675.0,GSM8020205 r1,0:101,A:1072507807;C:970584483;G:958817150;T:1055828545;N:5190,101,,,,1072507807,970584483,958817150,1055828545,5190,SRX23261673,SRS20163638,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29983,SRR27593008,SRX23261672,SRS20163637,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep10,GSM8020204,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep10,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types,GSM8020204,GSM8020204: hdlbpa  6 dpf  rep10; Danio rerio; RNA Seq,GSM8020204 r1,GSM8020204,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-wt_H14_S21_L002_R1_001.fastq.gz,fastq,5345570642.0,52926442.0,GSM8020204 r1,0:101,A:1439943379;C:1249929878;G:1229033309;T:1426645468;N:18608,101,,,,1439943379,1249929878,1229033309,1426645468,18608,SRX23261672,SRS20163637,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29984,SRR27593009,SRX23261671,SRS20163636,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep9,GSM8020203,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep9,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types,GSM8020203,GSM8020203: hdlbpa  6 dpf  rep9; Danio rerio; RNA Seq,GSM8020203 r1,GSM8020203,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-wt_H13_S20_L002_R1_001.fastq.gz,fastq,3927587101.0,38887001.0,GSM8020203 r1,0:101,A:1065676696;C:913744882;G:891757533;T:1056394325;N:13665,101,,,,1065676696,913744882,891757533,1056394325,13665,SRX23261671,SRS20163636,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29985,SRR27593010,SRX23261670,SRS20163635,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep8,GSM8020202,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep8,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types,GSM8020202,GSM8020202: hdlbpa  6 dpf  rep8; Danio rerio; RNA Seq,GSM8020202 r1,GSM8020202,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-wt_H12_S19_L002_R1_001.fastq.gz,fastq,6495421706.0,64311106.0,GSM8020202 r1,0:101,A:1776534004;C:1513743907;G:1447648946;T:1757472399;N:22450,101,,,,1776534004,1513743907,1447648946,1757472399,22450,SRX23261670,SRS20163635,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29986,SRR27593011,SRX23261669,SRS20163634,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep7,GSM8020201,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep7,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa wild types,GSM8020201,GSM8020201: hdlbpa  6 dpf  rep7; Danio rerio; RNA Seq,GSM8020201 r1,GSM8020201,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-wt_H11_S18_L002_R1_001.fastq.gz,fastq,3911576379.0,38728479.0,GSM8020201 r1,0:101,A:1058589544;C:907080870;G:898659386;T:1047232965;N:13614,101,,,,1058589544,907080870,898659386,1047232965,13614,SRX23261669,SRS20163634,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29987,SRR27593012,SRX23261668,SRS20163633,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep6,GSM8020200,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep6,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous,GSM8020200,GSM8020200: hdlbpa  6 dpf  rep6; Danio rerio; RNA Seq,GSM8020200 r1,GSM8020200,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-hom_H9_S16_L002_R1_001.fastq.gz,fastq,1927080000.0,19080000.0,GSM8020200 r1,0:101,A:523643390;C:445913624;G:440889014;T:516627902;N:6070,101,,,,523643390,445913624,440889014,516627902,6070,SRX23261668,SRS20163633,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29988,SRR27593013,SRX23261667,SRS20163632,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep5,GSM8020199,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep5,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous,GSM8020199,GSM8020199: hdlbpa  6 dpf  rep5; Danio rerio; RNA Seq,GSM8020199 r1,GSM8020199,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-hom_H8_S15_L002_R1_001.fastq.gz,fastq,1946049618.0,19267818.0,GSM8020199 r1,0:101,A:539909954;C:443888173;G:429627730;T:532616963;N:6798,101,,,,539909954,443888173,429627730,532616963,6798,SRX23261667,SRS20163632,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29989,SRR27593014,SRX23261666,SRS20163631,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep4,GSM8020198,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep4,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous,GSM8020198,GSM8020198: hdlbpa  6 dpf  rep4; Danio rerio; RNA Seq,GSM8020198 r1,GSM8020198,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-hom_H7_S14_L002_R1_001.fastq.gz,fastq,1039274749.0,10289849.0,GSM8020198 r1,0:101,A:283894686;C:241034413;G:233108651;T:281233307;N:3692,101,,,,283894686,241034413,233108651,281233307,3692,SRX23261666,SRS20163631,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29990,SRR27593015,SRX23261665,SRS20163630,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep3,GSM8020197,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep3,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa homozygous,GSM8020197,GSM8020197: hdlbpa  6 dpf  rep3; Danio rerio; RNA Seq,GSM8020197 r1,GSM8020197,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-hom_H10_S17_L002_R1_001.fastq.gz,fastq,4044191399.0,40041499.0,GSM8020197 r1,0:101,A:1104383207;C:936931840;G:907616152;T:1095246283;N:13917,101,,,,1104383207,936931840,907616152,1095246283,13917,SRX23261665,SRS20163630,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29991,SRR27593016,SRX23261664,SRS20163629,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep2,GSM8020196,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa heterozygous|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep2,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa heterozygous,GSM8020196,GSM8020196: hdlbpa  6 dpf  rep2; Danio rerio; RNA Seq,GSM8020196 r1,GSM8020196,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-het_H5_S13_L002_R1_001.fastq.gz,fastq,1470627771.0,14560671.0,GSM8020196 r1,0:101,A:405621136;C:336868389;G:326203713;T:401929517;N:5016,101,,,,405621136,336868389,326203713,401929517,5016,SRX23261664,SRS20163629,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29992,SRR27593017,SRX23261663,SRS20163628,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.,,,,hdlbpa  6 dpf  rep1,GSM8020195,,source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:hdlbpa heterozygous|geo loc name:missing|collection date:missing,hdlbpa  6 dpf  rep1,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  2 5 heads combined,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,tissue:head with eyes  2 5 heads combined|genotype:hdlbpa heterozygous,GSM8020195,GSM8020195: hdlbpa  6 dpf  rep1; Danio rerio; RNA Seq,GSM8020195 r1,GSM8020195,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,hdlbpa-6dpf-het_H3_S12_L002_R1_001.fastq.gz,fastq,1550552101.0,15352001.0,GSM8020195 r1,0:101,A:410548977;C:370146379;G:359721543;T:410129702;N:5500,101,,,,410548977,370146379,359721543,410129702,5500,SRX23261663,SRS20163628,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Larval,Larval,Multi-tissue,Multi-system
29995,SRR27593020,SRX23261660,SRS20163625,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  rep3,GSM8020144,,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  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,GSM8020144,GSM8020144: deaf1  6 dpf  rep3; Danio rerio; RNA Seq,GSM8020144 r1,GSM8020144,1,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_B5_S17_R1_001.fastq.gz,fastq,3381939247.0,33484547.0,GSM8020144 r1,0:101,A:875798724;C:822481757;G:801740363;T:881813538;N:104865,101,,,,875798724,822481757,801740363,881813538,104865,SRX23261660,SRS20163625,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
29996,SRR27593021,SRX23261659,SRS20163624,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  rep2,GSM8020143,,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  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,GSM8020143,GSM8020143: deaf1  6 dpf  rep2; Danio rerio; RNA Seq,GSM8020143 r1,GSM8020143,1,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_B4_S16_R1_001.fastq.gz,fastq,3326679319.0,32937419.0,GSM8020143 r1,0:101,A:857980796;C:816006644;G:796253045;T:856335882;N:102952,101,,,,857980796,816006644,796253045,856335882,102952,SRX23261659,SRS20163624,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
29997,SRR27593022,SRX23261658,SRS20163623,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  rep1,GSM8020142,,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  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,GSM8020142,GSM8020142: deaf1  6 dpf  rep1; Danio rerio; RNA Seq,GSM8020142 r1,GSM8020142,1,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_B3_S15_R1_001.fastq.gz,fastq,3904797360.0,38661360.0,GSM8020142 r1,0:101,A:1006598239;C:958631421;G:931480760;T:1007966467;N:120473,101,,,,1006598239,958631421,931480760,1007966467,120473,SRX23261658,SRS20163623,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
33696,SRR30599775,SRX26022476,SRS22594195,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a wt  5 dpf  rep 2,GSM8504328,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing,ebf3a wt  5 dpf  rep 2,Paired 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  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types,GSM8504328,GSM8504328: ebf3a wt  5 dpf  rep 2; Danio rerio; RNA Seq,GSM8504328 r1,GSM8504328,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-WT-2-5dpf_R1_001.fastq.gz Ebf-WT-2-5dpf_R2_001.fastq.gz,fastq fastq,17620546500.0,58735155.0,GSM8504328 r1,0:150 1:150,A:4442356407;C:4365499245;G:4407165860;T:4405169272;N:355716,150,150,,,4442356407,4365499245,4407165860,4405169272,355716,SRX26022476,SRS22594195,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33697,SRR30599776,SRX26022475,SRS22594194,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a wt  5 dpf  rep 1,GSM8504327,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing,ebf3a wt  5 dpf  rep 1,Paired 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  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types,GSM8504327,GSM8504327: ebf3a wt  5 dpf  rep 1; Danio rerio; RNA Seq,GSM8504327 r1,GSM8504327,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-WT-1-5dpf_R1_001.fastq.gz Ebf-WT-1-5dpf_R2_001.fastq.gz,fastq fastq,14881331700.0,49604439.0,GSM8504327 r1,0:150 1:150,A:3819750403;C:3611501542;G:3658667991;T:3791111572;N:300192,150,150,,,3819750403,3611501542,3658667991,3791111572,300192,SRX26022475,SRS22594194,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33698,SRR30599777,SRX26022474,SRS22594193,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a hom  5 dpf  rep 2,GSM8504326,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing,ebf3a hom  5 dpf  rep 2,Paired 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  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous,GSM8504326,GSM8504326: ebf3a hom  5 dpf  rep 2; Danio rerio; RNA Seq,GSM8504326 r1,GSM8504326,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-Homo-2-5dpf_R1_001.fastq.gz Ebf-Homo-2-5dpf_R2_001.fastq.gz,fastq fastq,13980599100.0,46601997.0,GSM8504326 r1,0:150 1:150,A:3559157122;C:3432017726;G:3462680948;T:3526461889;N:281415,150,150,,,3559157122,3432017726,3462680948,3526461889,281415,SRX26022474,SRS22594193,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33699,SRR30599778,SRX26022473,SRS22594192,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a hom  5 dpf  rep 1,GSM8504325,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing,ebf3a hom  5 dpf  rep 1,Paired 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  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous,GSM8504325,GSM8504325: ebf3a hom  5 dpf  rep 1; Danio rerio; RNA Seq,GSM8504325 r1,GSM8504325,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-Homo-1-5dpf_R1_001.fastq.gz Ebf-Homo-1-5dpf_R2_001.fastq.gz,fastq fastq,16257229800.0,54190766.0,GSM8504325 r1,0:150 1:150,A:4127739980;C:3994508761;G:4048290353;T:4086361510;N:329196,150,150,,,4127739980,3994508761,4048290353,4086361510,329196,SRX26022473,SRS22594192,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33900,SRR30879294,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L001_I1_001.fastq.gz TKO_dsRED_S2_L001_I2_001.fastq.gz TKO_dsRED_S2_L001_R1_001.fastq.gz TKO_dsRED_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,3764848932.0,27281514.0,GSM8553899 r1,0:10 1:10 2:28 3:90,A:692470222;C:567540605;G:576111845;T:618305574;N:908014,10,10,28,90,692470222,567540605,576111845,618305574,908014,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33901,SRR30879295,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L002_I1_001.fastq.gz TKO_dsRED_S2_L002_I2_001.fastq.gz TKO_dsRED_S2_L002_R1_001.fastq.gz TKO_dsRED_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3726674544.0,27004888.0,GSM8553899 r2,0:10 1:10 2:28 3:90,A:685914766;C:561837246;G:569990126;T:611748773;N:949009,10,10,28,90,685914766,561837246,569990126,611748773,949009,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33902,SRR30879296,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L003_I1_001.fastq.gz TKO_dsRED_S2_L003_I2_001.fastq.gz TKO_dsRED_S2_L003_R1_001.fastq.gz TKO_dsRED_S2_L003_R2_001.fastq.gz,fastq fastq fastq fastq,3722937918.0,26977811.0,GSM8553899 r3,0:10 1:10 2:28 3:90,A:676537253;C:555568581;G:563937331;T:604713745;N:27246080,10,10,28,90,676537253,555568581,563937331,604713745,27246080,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33903,SRR30879297,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L004_I1_001.fastq.gz TKO_dsRED_S2_L004_I2_001.fastq.gz TKO_dsRED_S2_L004_R1_001.fastq.gz TKO_dsRED_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3758183394.0,27233213.0,GSM8553899 r4,0:10 1:10 2:28 3:90,A:692108990;C:566665777;G:574900426;T:617012755;N:301222,10,10,28,90,692108990,566665777,574900426,617012755,301222,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33904,SRR30879298,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L001_I1_001.fastq.gz WT_dsRED_S1_L001_I2_001.fastq.gz WT_dsRED_S1_L001_R1_001.fastq.gz WT_dsRED_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4039025952.0,29268304.0,GSM8553898 r1,0:10 1:10 2:28 3:90,A:743074639;C:613897517;G:610150022;T:666064959;N:960223,10,10,28,90,743074639,613897517,610150022,666064959,960223,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33905,SRR30879299,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L002_I1_001.fastq.gz WT_dsRED_S1_L002_I2_001.fastq.gz WT_dsRED_S1_L002_R1_001.fastq.gz WT_dsRED_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3995500476.0,28952902.0,GSM8553898 r2,0:10 1:10 2:28 3:90,A:735710467;C:607339644;G:603122849;T:658578339;N:1009881,10,10,28,90,735710467,607339644,603122849,658578339,1009881,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33906,SRR30879300,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L003_I1_001.fastq.gz WT_dsRED_S1_L003_I2_001.fastq.gz WT_dsRED_S1_L003_R1_001.fastq.gz WT_dsRED_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,3989006196.0,28905842.0,GSM8553898 r3,0:10 1:10 2:28 3:90,A:725297656;C:600094089;G:596392169;T:650543321;N:29198545,10,10,28,90,725297656,600094089,596392169,650543321,29198545,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33907,SRR30879301,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L004_I1_001.fastq.gz WT_dsRED_S1_L004_I2_001.fastq.gz WT_dsRED_S1_L004_R1_001.fastq.gz WT_dsRED_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,4028525946.0,29192217.0,GSM8553898 r4,0:10 1:10 2:28 3:90,A:742291215;C:612398679;G:608091658;T:664191759;N:326219,10,10,28,90,742291215,612398679,608091658,664191759,326219,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
34650,SRR32153232,SRX27498881,SRS23919995,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep8,GSM8761756,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings,GSM8761756,GSM8761756: kalta4  6 dpf  rep8; Danio rerio; RNA Seq,GSM8761756 r1,GSM8761756,1,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,,SRP560400,,,WT_8_S29_R1_001.fastq.gz,fastq,5627327211.0,55716111.0,GSM8761756 r1,0:101,A:1483734097;C:1355935398;G:1309419099;T:1478203668;N:34949,101,,,,1483734097,1355935398,1309419099,1478203668,34949,SRX27498881,SRS23919995,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34651,SRR32153233,SRX27498880,SRS23919994,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep7,GSM8761755,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings,GSM8761755,GSM8761755: kalta4  6 dpf  rep7; Danio rerio; RNA Seq,GSM8761755 r1,GSM8761755,1,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,,SRP560400,,,WT_7_S28_R1_001.fastq.gz,fastq,5650914751.0,55949651.0,GSM8761755 r1,0:101,A:1479986179;C:1371193880;G:1334717286;T:1464984021;N:33385,101,,,,1479986179,1371193880,1334717286,1464984021,33385,SRX27498880,SRS23919994,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34652,SRR32153234,SRX27498879,SRS23919993,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep6,GSM8761754,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings,GSM8761754,GSM8761754: kalta4  6 dpf  rep6; Danio rerio; RNA Seq,GSM8761754 r1,GSM8761754,1,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,,SRP560400,,,WT_6_S27_R1_001.fastq.gz,fastq,5635658196.0,55798596.0,GSM8761754 r1,0:101,A:1459951969;C:1372576688;G:1347555952;T:1455538617;N:34970,101,,,,1459951969,1372576688,1347555952,1455538617,34970,SRX27498879,SRS23919993,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34653,SRR32153235,SRX27498878,SRS23919992,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep5,GSM8761753,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 wildtype siblings,GSM8761753,GSM8761753: kalta4  6 dpf  rep5; Danio rerio; RNA Seq,GSM8761753 r1,GSM8761753,1,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,,SRP560400,,,WT_5_S26_R1_001.fastq.gz,fastq,5922774835.0,58641335.0,GSM8761753 r1,0:101,A:1566649690;C:1415187133;G:1381930008;T:1558970790;N:37214,101,,,,1566649690,1415187133,1381930008,1558970790,37214,SRX27498878,SRS23919992,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34654,SRR32153236,SRX27498877,SRS23919989,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep4,GSM8761752,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic,GSM8761752,GSM8761752: kalta4  6 dpf  rep4; Danio rerio; RNA Seq,GSM8761752 r1,GSM8761752,1,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,,SRP560400,,,KALTA4_4_S25_R1_001.fastq.gz,fastq,6047928379.0,59880479.0,GSM8761752 r1,0:101,A:1569269410;C:1490723359;G:1447592225;T:1540306370;N:37015,101,,,,1569269410,1490723359,1447592225,1540306370,37015,SRX27498877,SRS23919989,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34655,SRR32153237,SRX27498876,SRS23919990,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep3,GSM8761751,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic,GSM8761751,GSM8761751: kalta4  6 dpf  rep3; Danio rerio; RNA Seq,GSM8761751 r1,GSM8761751,1,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,,SRP560400,,,KALTA4_3_S24_R1_001.fastq.gz,fastq,6691826306.0,66255706.0,GSM8761751 r1,0:101,A:1754018100;C:1609587760;G:1575245791;T:1752933196;N:41459,101,,,,1754018100,1609587760,1575245791,1752933196,41459,SRX27498876,SRS23919990,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34656,SRR32153238,SRX27498875,SRS23919991,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep2,GSM8761750,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic,GSM8761750,GSM8761750: kalta4  6 dpf  rep2; Danio rerio; RNA Seq,GSM8761750 r1,GSM8761750,1,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,,SRP560400,,,KALTA4_2_S23_R1_001.fastq.gz,fastq,3766378981.0,37290881.0,GSM8761750 r1,0:101,A:984999095;C:907081679;G:917777211;T:956510200;N:10796,101,,,,984999095,907081679,917777211,956510200,10796,SRX27498875,SRS23919991,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
34657,SRR32153239,SRX27498874,SRS23919988,SRP560400,PRJNA1216611,Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4,GSE288241,Transcriptome Analysis,The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: RNA sequencing of dissected heads of larval zebrafish of the TGelavl3:KalTA4 zebrafish versus wildtype siblings.,,,,kalta4  6 dpf  rep1,GSM8761749,,source name:head with eyes  3 5 heads combined|tissue:head with eyes  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic|geo loc name:missing|collection date:missing,kalta4  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  3 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  3 5 heads combined|genotype:elavl3:kalta4 heterozygous transgenic,GSM8761749,GSM8761749: kalta4  6 dpf  rep1; Danio rerio; RNA Seq,GSM8761749 r1,GSM8761749,1,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,,SRP560400,,,KALTA4_1_S22_R1_001.fastq.gz,fastq,5711770382.0,56552182.0,GSM8761749 r1,0:101,A:1464917319;C:1416415848;G:1380626453;T:1449775282;N:35480,101,,,,1464917319,1416415848,1380626453,1449775282,35480,SRX27498874,SRS23919988,SRA2063313,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,2025-01-28,Larval,Larval,Multi-tissue,Multi-system
35872,SRR33167499,SRX28428353,SRS24751225,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1H L6.D705,GSM8919409,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1H L6.D705,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919409,GSM8919409: MB125 1H L6.D705; Danio rerio; RNA Seq,GSM8919409 r1,GSM8919409,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1H_L6.D705_1.fastq.gz MB125_1H_L6.D705_2.fastq.gz,fastq fastq,2373981966.0,23274333.0,GSM8919409 r1,0:51 1:51,A:568938101;C:599603085;G:595620007;T:609800208;N:20565,51,51,,,568938101,599603085,595620007,609800208,20565,SRX28428353,SRS24751225,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35873,SRR33167500,SRX28428352,SRS24751226,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1G L6.D707,GSM8919408,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1G L6.D707,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919408,GSM8919408: MB125 1G L6.D707; Danio rerio; RNA Seq,GSM8919408 r1,GSM8919408,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1G_L6.D707_1.fastq.gz MB125_1G_L6.D707_2.fastq.gz,fastq fastq,2557560036.0,25074118.0,GSM8919408 r1,0:51 1:51,A:619676841;C:640365331;G:637208159;T:660287312;N:22393,51,51,,,619676841,640365331,637208159,660287312,22393,SRX28428352,SRS24751226,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35874,SRR33167501,SRX28428351,SRS24751224,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1F L6.D706,GSM8919407,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1F L6.D706,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919407,GSM8919407: MB125 1F L6.D706; Danio rerio; RNA Seq,GSM8919407 r1,GSM8919407,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1F_L6.D706_1.fastq.gz MB125_1F_L6.D706_2.fastq.gz,fastq fastq,2646607362.0,25947131.0,GSM8919407 r1,0:51 1:51,A:620307465;C:682923030;G:678065242;T:665289569;N:22056,51,51,,,620307465,682923030,678065242,665289569,22056,SRX28428351,SRS24751224,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35875,SRR33167502,SRX28428350,SRS24751223,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1D L6.D703,GSM8919406,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1D L6.D703,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919406,GSM8919406: MB125 1D L6.D703; Danio rerio; RNA Seq,GSM8919406 r1,GSM8919406,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1D_L6.D703_1.fastq.gz MB125_1D_L6.D703_2.fastq.gz,fastq fastq,2431917150.0,23842325.0,GSM8919406 r1,0:51 1:51,A:589729741;C:608847610;G:603837645;T:629482079;N:20075,51,51,,,589729741,608847610,603837645,629482079,20075,SRX28428350,SRS24751223,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35876,SRR33167503,SRX28428349,SRS24751222,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1C L6.D704,GSM8919405,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1C L6.D704,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919405,GSM8919405: MB125 1C L6.D704; Danio rerio; RNA Seq,GSM8919405 r1,GSM8919405,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1C_L6.D704_1.fastq.gz MB125_1C_L6.D704_2.fastq.gz,fastq fastq,2525909130.0,24763815.0,GSM8919405 r1,0:51 1:51,A:624391801;C:621947668;G:618750869;T:660797379;N:21413,51,51,,,624391801,621947668,618750869,660797379,21413,SRX28428349,SRS24751222,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35877,SRR33167504,SRX28428348,SRS24751221,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1A L6.D702,GSM8919404,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1A L6.D702,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919404,GSM8919404: MB125 1A L6.D702; Danio rerio; RNA Seq,GSM8919404 r1,GSM8919404,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1A_L6.D702_1.fastq.gz MB125_1A_L6.D702_2.fastq.gz,fastq fastq,2374806432.0,23282416.0,GSM8919404 r1,0:51 1:51,A:570636423;C:598720207;G:596247498;T:609181713;N:20591,51,51,,,570636423,598720207,596247498,609181713,20591,SRX28428348,SRS24751221,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35878,SRR33167505,SRX28428347,SRS24751220,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC7 S1,GSM8919403,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC7 S1,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919403,GSM8919403: GRC355 CC7 S1; Danio rerio; RNA Seq,GSM8919403 r1,GSM8919403,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC7_S1_R1_001.fastq.gz,fastq,1602530400.0,21367072.0,GSM8919403 r1,0:75,A:423908384;C:380610264;G:430749077;T:367248932;N:13743,75,,,,423908384,380610264,430749077,367248932,13743,SRX28428347,SRS24751220,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35879,SRR33167506,SRX28428346,SRS24751219,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC6 S13,GSM8919402,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC6 S13,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919402,GSM8919402: GRC355 CC6 S13; Danio rerio; RNA Seq,GSM8919402 r1,GSM8919402,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC6_S13_R1_001.fastq.gz,fastq,2682385275.0,35765137.0,GSM8919402 r1,0:75,A:714420635;C:641843546;G:710142891;T:615939845;N:38358,75,,,,714420635,641843546,710142891,615939845,38358,SRX28428346,SRS24751219,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35880,SRR33167507,SRX28428345,SRS24751218,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC5 S9,GSM8919401,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC5 S9,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919401,GSM8919401: GRC355 CC5 S9; Danio rerio; RNA Seq,GSM8919401 r1,GSM8919401,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC5_S9_R1_001.fastq.gz,fastq,1963794750.0,26183930.0,GSM8919401 r1,0:75,A:526554394;C:453867368;G:498987697;T:484357818;N:27473,75,,,,526554394,453867368,498987697,484357818,27473,SRX28428345,SRS24751218,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35881,SRR33167508,SRX28428344,SRS24751217,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC4 S6,GSM8919400,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC4 S6,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919400,GSM8919400: GRC355 CC4 S6; Danio rerio; RNA Seq,GSM8919400 r1,GSM8919400,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC4_S6_R1_001.fastq.gz,fastq,2337900150.0,31172002.0,GSM8919400 r1,0:75,A:616059883;C:562202412;G:623837969;T:535779947;N:19939,75,,,,616059883,562202412,623837969,535779947,19939,SRX28428344,SRS24751217,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system