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
44,DRR668250,DRX648352,DRS458865,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 3,Zebrafish 2wpi 3,SAMD00799623,,sample name:Zebrafish 2wpi 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 25|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799623,DRX648352,RNA seq of spinal cord in zebrafish at 2wpi injured 3,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799623,,,,14782516800.0,73912584.0,DRR668250,0:100 1:100,A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943,100,100,,,4058090278,3335994894,3323563782,4062467903,2399943,DRX648352,DRS458865,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
45,DRR668249,DRX648351,DRS458864,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 2,Zebrafish 2wpi 2,SAMD00799622,,sample name:Zebrafish 2wpi 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799622,DRX648351,RNA seq of spinal cord in zebrafish at 2wpi injured 2,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799622,,,,13687641800.0,68438209.0,DRR668249,0:100 1:100,A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902,100,100,,,3759784620,3087398782,3083881581,3754378915,2197902,DRX648351,DRS458864,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
46,DRR668248,DRX648350,DRS458863,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 1,Zebrafish 2wpi 1,SAMD00799621,,sample name:Zebrafish 2wpi 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799621,DRX648350,RNA seq of spinal cord in zebrafish at 2wpi injured 1,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799621,,,,16376197200.0,81880986.0,DRR668248,0:100 1:100,A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189,100,100,,,4485868844,3700974430,3710833937,4475827800,2692189,DRX648350,DRS458863,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
47,DRR668247,DRX648349,DRS458862,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 3,Zebrafish Control 3,SAMD00799620,,sample name:Zebrafish Control 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799620,DRX648349,RNA seq of spinal cord in zebrafish at 0wpi control 3,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799620,,,,13377538600.0,66887693.0,DRR668247,0:100 1:100,A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800,100,100,,,3725064764,2973653932,2980883214,3695767890,2168800,DRX648349,DRS458862,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
48,DRR668246,DRX648348,DRS458861,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 2,Zebrafish Control 2,SAMD00799619,,sample name:Zebrafish Control 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799619,DRX648348,RNA seq of spinal cord in zebrafish at 0wpi control 2,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799619,,,,14971411400.0,74857057.0,DRR668246,0:100 1:100,A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904,100,100,,,4160326445,3329083037,3329123314,4150453700,2424904,DRX648348,DRS458861,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
49,DRR668245,DRX648347,DRS458860,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 1,Zebrafish Control 1,SAMD00799618,,sample name:Zebrafish Control 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2024 05 04|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799618,DRX648347,RNA seq of spinal cord in zebrafish at 0wpi control 1,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799618,,,,13912523800.0,69562619.0,DRR668245,0:100 1:100,A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776,100,100,,,3888902049,3079617959,3075111814,3866655202,2236776,DRX648347,DRS458860,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
26386,SRR25917801,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L01_R1_001.fastq.gz 22-02953_S24_L01_R2_001.fastq.gz,fastq fastq,1889616596.0,9640901.0,GSM7761847 r1,0:98 1:98,A:502776047;C:437946838;G:435110760;T:512766381;N:1016570,98,98,,,502776047,437946838,435110760,512766381,1016570,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9328,0.92722,0.09638,0.09803,0.70285,0.70345,0.50688,0.50192,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26387,SRR25917802,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L02_R1_001.fastq.gz 22-02953_S24_L02_R2_001.fastq.gz,fastq fastq,2862274828.0,14603443.0,GSM7761847 r2,0:98 1:98,A:757126187;C:668245308;G:664888408;T:771615407;N:399518,98,98,,,757126187,668245308,664888408,771615407,399518,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94091,0.93645,0.09729,0.09803,0.70309,0.7041,0.51085,0.50502,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26388,SRR25917803,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L03_R1_001.fastq.gz 22-02953_S24_L03_R2_001.fastq.gz,fastq fastq,2584726676.0,13187381.0,GSM7761847 r3,0:98 1:98,A:684660799;C:601450975;G:598598564;T:699408337;N:608001,98,98,,,684660799,601450975,598598564,699408337,608001,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94069,0.93734,0.09389,0.09545,0.70264,0.70254,0.49261,0.50213,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26389,SRR25917804,SRX21637674,SRS18807763,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02953,GSM7761847,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02953,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5,GSM7761847,GSM7761847: 22 02953; Danio rerio; RNA Seq,GSM7761847 r1,GSM7761847,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02953_S24_L04_R1_001.fastq.gz 22-02953_S24_L04_R2_001.fastq.gz,fastq fastq,4100821760.0,20922560.0,GSM7761847 r4,0:98 1:98,A:1082079470;C:958686210;G:956517599;T:1103432545;N:105936,98,98,,,1082079470,958686210,956517599,1103432545,105936,SRX21637674,SRS18807763,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94702,0.94327,0.09591,0.09712,0.70252,0.70402,0.51264,0.51319,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26390,SRR25917805,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L01_R1_001.fastq.gz 22-02952_S23_L01_R2_001.fastq.gz,fastq fastq,1992642428.0,10166543.0,GSM7761846 r1,0:98 1:98,A:531507040;C:460525641;G:457631907;T:541925633;N:1052207,98,98,,,531507040,460525641,457631907,541925633,1052207,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93066,0.92518,0.10299,0.10378,0.7067,0.70735,0.49353,0.49352,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26391,SRR25917806,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L02_R1_001.fastq.gz 22-02952_S23_L02_R2_001.fastq.gz,fastq fastq,2995445852.0,15282887.0,GSM7761846 r2,0:98 1:98,A:793690840;C:697826413;G:694428368;T:809079956;N:420275,98,98,,,793690840,697826413,694428368,809079956,420275,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93866,0.93421,0.10232,0.10415,0.7038,0.70496,0.49446,0.49935,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26392,SRR25917807,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L03_R1_001.fastq.gz 22-02952_S23_L03_R2_001.fastq.gz,fastq fastq,2558248644.0,13052289.0,GSM7761846 r3,0:98 1:98,A:678550810;C:594295508;G:591607450;T:693175940;N:618936,98,98,,,678550810,594295508,591607450,693175940,618936,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93834,0.93526,0.10036,0.10226,0.70443,0.70565,0.49418,0.4945,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26393,SRR25917808,SRX21637673,SRS18807762,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02952,GSM7761846,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing,22 02952,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8,GSM7761846,GSM7761846: 22 02952; Danio rerio; RNA Seq,GSM7761846 r1,GSM7761846,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02952_S23_L04_R1_001.fastq.gz 22-02952_S23_L04_R2_001.fastq.gz,fastq fastq,3963250536.0,20220666.0,GSM7761846 r4,0:98 1:98,A:1045663273;C:926206212;G:924140110;T:1067139742;N:101199,98,98,,,1045663273,926206212,924140110,1067139742,101199,SRX21637673,SRS18807762,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94449,0.94083,0.10086,0.10197,0.70469,0.70569,0.4991,0.49202,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26394,SRR25917809,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L01_R1_001.fastq.gz 22-02951_S22_L01_R2_001.fastq.gz,fastq fastq,2029687408.0,10355548.0,GSM7761845 r1,0:98 1:98,A:538688097;C:471579919;G:470623522;T:547765689;N:1030181,98,98,,,538688097,471579919,470623522,547765689,1030181,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.92721,0.92969,0.09472,0.09676,0.70423,0.70276,0.49981,0.49898,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26395,SRR25917810,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L02_R1_001.fastq.gz 22-02951_S22_L02_R2_001.fastq.gz,fastq fastq,3072360760.0,15675310.0,GSM7761845 r2,0:98 1:98,A:810685642;C:719109817;G:718137072;T:824036555;N:391674,98,98,,,810685642,719109817,718137072,824036555,391674,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9358,0.93813,0.09385,0.09614,0.70341,0.70303,0.49098,0.49194,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26396,SRR25917811,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L03_R1_001.fastq.gz 22-02951_S22_L03_R2_001.fastq.gz,fastq fastq,2765019432.0,14107242.0,GSM7761845 r3,0:98 1:98,A:730929526;C:644675885;G:644121852;T:744649936;N:642233,98,98,,,730929526,644675885,644121852,744649936,642233,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93375,0.93756,0.0926,0.09517,0.70429,0.70358,0.50064,0.50166,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26397,SRR25917812,SRX21637672,SRS18807761,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02951,GSM7761845,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing,22 02951,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7,GSM7761845,GSM7761845: 22 02951; Danio rerio; RNA Seq,GSM7761845 r1,GSM7761845,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02951_S22_L04_R1_001.fastq.gz 22-02951_S22_L04_R2_001.fastq.gz,fastq fastq,4491524436.0,22915941.0,GSM7761845 r4,0:98 1:98,A:1183373286;C:1051469132;G:1052482979;T:1204083766;N:115273,98,98,,,1183373286,1051469132,1052482979,1204083766,115273,SRX21637672,SRS18807761,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94091,0.94403,0.09318,0.09521,0.70374,0.70234,0.49577,0.49187,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26398,SRR25917813,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L01_R1_001.fastq.gz 22-02949_S21_L01_R2_001.fastq.gz,fastq fastq,2534565376.0,12931456.0,GSM7761844 r1,0:98 1:98,A:674884849;C:586725099;G:584045434;T:687552587;N:1357407,98,98,,,674884849,586725099,584045434,687552587,1357407,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93278,0.9279,0.10047,0.10166,0.70506,0.70461,0.51365,0.5138,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26399,SRR25917814,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L02_R1_001.fastq.gz 22-02949_S21_L02_R2_001.fastq.gz,fastq fastq,3889732308.0,19845573.0,GSM7761844 r2,0:98 1:98,A:1029905526;C:906662466;G:903535838;T:1049088768;N:539710,98,98,,,1029905526,906662466,903535838,1049088768,539710,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94166,0.93609,0.09893,0.10006,0.70313,0.70439,0.51404,0.50855,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26400,SRR25917815,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L03_R1_001.fastq.gz 22-02949_S21_L03_R2_001.fastq.gz,fastq fastq,3291066380.0,16791155.0,GSM7761844 r3,0:98 1:98,A:872393079;C:764845510;G:762405303;T:890638586;N:783902,98,98,,,872393079,764845510,762405303,890638586,783902,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94062,0.93691,0.09836,0.0996,0.70416,0.70461,0.51782,0.50965,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26401,SRR25917816,SRX21637671,SRS18807760,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02949,GSM7761844,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing,22 02949,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7,GSM7761844,GSM7761844: 22 02949; Danio rerio; RNA Seq,GSM7761844 r1,GSM7761844,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02949_S21_L04_R1_001.fastq.gz 22-02949_S21_L04_R2_001.fastq.gz,fastq fastq,5366313988.0,27379153.0,GSM7761844 r4,0:98 1:98,A:1415961559;C:1253439804;G:1252742067;T:1444033449;N:137109,98,98,,,1415961559,1253439804,1252742067,1444033449,137109,SRX21637671,SRS18807760,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94568,0.94293,0.09906,0.10054,0.70402,0.7052,0.51461,0.52073,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26402,SRR25917817,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L01_R1_001.fastq.gz 22-02948_S20_L01_R2_001.fastq.gz,fastq fastq,2053905168.0,10479108.0,GSM7761843 r1,0:98 1:98,A:547671134;C:475089537;G:473080534;T:556992811;N:1071152,98,98,,,547671134,475089537,473080534,556992811,1071152,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93522,0.9298,0.10197,0.10238,0.70339,0.70421,0.50454,0.50393,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26403,SRR25917818,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L02_R1_001.fastq.gz 22-02948_S20_L02_R2_001.fastq.gz,fastq fastq,3144952300.0,16045675.0,GSM7761843 r2,0:98 1:98,A:832655138;C:733701092;G:731348360;T:846811030;N:436680,98,98,,,832655138,733701092,731348360,846811030,436680,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94365,0.93984,0.10028,0.10124,0.70398,0.70565,0.50353,0.50505,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26404,SRR25917819,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L03_R1_001.fastq.gz 22-02948_S20_L03_R2_001.fastq.gz,fastq fastq,2460170244.0,12551889.0,GSM7761843 r3,0:98 1:98,A:651706233;C:572474025;G:570982999;T:664399947;N:607040,98,98,,,651706233,572474025,570982999,664399947,607040,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9411,0.93886,0.09891,0.10006,0.70485,0.70362,0.50337,0.50208,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26405,SRR25917820,SRX21637670,SRS18807759,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02948,GSM7761843,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02948,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761843,GSM7761843: 22 02948; Danio rerio; RNA Seq,GSM7761843 r1,GSM7761843,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02948_S20_L04_R1_001.fastq.gz 22-02948_S20_L04_R2_001.fastq.gz,fastq fastq,3890916344.0,19851614.0,GSM7761843 r4,0:98 1:98,A:1025556861;C:910441322;G:909593603;T:1045230061;N:94497,98,98,,,1025556861,910441322,909593603,1045230061,94497,SRX21637670,SRS18807759,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94835,0.94517,0.09781,0.09849,0.70274,0.70374,0.5027,0.5008,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26406,SRR25917821,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L01_R1_001.fastq.gz 22-02947_S19_L01_R2_001.fastq.gz,fastq fastq,1696563848.0,8655938.0,GSM7761842 r1,0:98 1:98,A:453186259;C:391677304;G:390304899;T:460508753;N:886633,98,98,,,453186259,391677304,390304899,460508753,886633,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9329,0.92803,0.10284,0.10415,0.70611,0.70664,0.49615,0.49305,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26407,SRR25917822,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L02_R1_001.fastq.gz 22-02947_S19_L02_R2_001.fastq.gz,fastq fastq,2634385040.0,13440740.0,GSM7761842 r2,0:98 1:98,A:699185241;C:613094915;G:611213748;T:710534569;N:356567,98,98,,,699185241,613094915,611213748,710534569,356567,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94184,0.93645,0.10113,0.10207,0.70268,0.70345,0.50894,0.50924,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26408,SRR25917823,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L03_R1_001.fastq.gz 22-02947_S19_L03_R2_001.fastq.gz,fastq fastq,2356722424.0,12024094.0,GSM7761842 r3,0:98 1:98,A:626784832;C:546121522;G:545024526;T:638243477;N:548067,98,98,,,626784832,546121522,545024526,638243477,548067,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94068,0.93749,0.09906,0.10122,0.7039,0.70449,0.50662,0.51119,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26409,SRR25917824,SRX21637669,SRS18807758,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02947,GSM7761842,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing,22 02947,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6,GSM7761842,GSM7761842: 22 02947; Danio rerio; RNA Seq,GSM7761842 r1,GSM7761842,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02947_S19_L04_R1_001.fastq.gz 22-02947_S19_L04_R2_001.fastq.gz,fastq fastq,3824206372.0,19511257.0,GSM7761842 r4,0:98 1:98,A:1013047237;C:890237600;G:890115590;T:1030706585;N:99360,98,98,,,1013047237,890237600,890115590,1030706585,99360,SRX21637669,SRS18807758,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9463,0.94321,0.10017,0.1014,0.7038,0.70437,0.50533,0.51168,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26410,SRR25917825,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L01_R1_001.fastq.gz 22-02946_S18_L01_R2_001.fastq.gz,fastq fastq,2024888936.0,10331066.0,GSM7761841 r1,0:98 1:98,A:542606378;C:466454644;G:464323282;T:550429046;N:1075586,98,98,,,542606378,466454644,464323282,550429046,1075586,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.933,0.92706,0.10233,0.10303,0.70429,0.70465,0.49443,0.48878,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26411,SRR25917826,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L02_R1_001.fastq.gz 22-02946_S18_L02_R2_001.fastq.gz,fastq fastq,3069224368.0,15659308.0,GSM7761841 r2,0:98 1:98,A:816848746;C:712756904;G:710416167;T:828782508;N:420043,98,98,,,816848746,712756904,710416167,828782508,420043,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94117,0.93483,0.10216,0.10274,0.70467,0.7051,0.50931,0.51613,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26412,SRR25917827,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L03_R1_001.fastq.gz 22-02946_S18_L03_R2_001.fastq.gz,fastq fastq,2612758008.0,13330398.0,GSM7761841 r3,0:98 1:98,A:695834172;C:605270278;G:603512924;T:707518532;N:622102,98,98,,,695834172,605270278,603512924,707518532,622102,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94095,0.93716,0.09929,0.10092,0.70343,0.70396,0.49363,0.50028,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26413,SRR25917828,SRX21637668,SRS18807757,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02946,GSM7761841,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing,22 02946,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5,GSM7761841,GSM7761841: 22 02946; Danio rerio; RNA Seq,GSM7761841 r1,GSM7761841,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02946_S18_L04_R1_001.fastq.gz 22-02946_S18_L04_R2_001.fastq.gz,fastq fastq,4163040196.0,21240001.0,GSM7761841 r4,0:98 1:98,A:1104116525;C:968916166;G:968183447;T:1121718793;N:105265,98,98,,,1104116525,968916166,968183447,1121718793,105265,SRX21637668,SRS18807757,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94611,0.94219,0.09973,0.10107,0.70303,0.70394,0.51684,0.51536,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26414,SRR25917829,SRX21637667,SRS18807756,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02945,GSM7761840,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing,22 02945,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2,GSM7761840,GSM7761840: 22 02945; Danio rerio; RNA Seq,GSM7761840 r1,GSM7761840,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02945_S17_L01_R1_001.fastq.gz 22-02945_S17_L01_R2_001.fastq.gz,fastq fastq,2619858892.0,13366627.0,GSM7761840 r1,0:98 1:98,A:705166138;C:600115338;G:598330950;T:714861086;N:1385380,98,98,,,705166138,600115338,598330950,714861086,1385380,SRX21637667,SRS18807756,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93476,0.92831,0.09718,0.09862,0.70457,0.70567,0.4957,0.52808,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26415,SRR25917830,SRX21637667,SRS18807756,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02945,GSM7761840,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing,22 02945,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2,GSM7761840,GSM7761840: 22 02945; Danio rerio; RNA Seq,GSM7761840 r1,GSM7761840,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02945_S17_L02_R1_001.fastq.gz 22-02945_S17_L02_R2_001.fastq.gz,fastq fastq,3955690816.0,20182096.0,GSM7761840 r2,0:98 1:98,A:1058443729;C:912805409;G:911028821;T:1072858146;N:554711,98,98,,,1058443729,912805409,911028821,1072858146,554711,SRX21637667,SRS18807756,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94318,0.93872,0.09645,0.0973,0.70613,0.70715,0.52714,0.52457,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26416,SRR25917831,SRX21637667,SRS18807756,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02945,GSM7761840,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing,22 02945,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2,GSM7761840,GSM7761840: 22 02945; Danio rerio; RNA Seq,GSM7761840 r1,GSM7761840,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02945_S17_L03_R1_001.fastq.gz 22-02945_S17_L03_R2_001.fastq.gz,fastq fastq,3434879028.0,17524893.0,GSM7761840 r3,0:98 1:98,A:919933771;C:790247133;G:789182712;T:934693677;N:821735,98,98,,,919933771,790247133,789182712,934693677,821735,SRX21637667,SRS18807756,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94324,0.93862,0.09659,0.09728,0.70571,0.70583,0.52686,0.53004,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26417,SRR25917832,SRX21637667,SRS18807756,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02945,GSM7761840,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing,22 02945,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2,GSM7761840,GSM7761840: 22 02945; Danio rerio; RNA Seq,GSM7761840 r1,GSM7761840,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02945_S17_L04_R1_001.fastq.gz 22-02945_S17_L04_R2_001.fastq.gz,fastq fastq,5433098048.0,27719888.0,GSM7761840 r4,0:98 1:98,A:1449452101;C:1255780383;G:1256728807;T:1470998035;N:138722,98,98,,,1449452101,1255780383,1256728807,1470998035,138722,SRX21637667,SRS18807756,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94785,0.94392,0.09527,0.09667,0.70556,0.70676,0.52907,0.52805,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26418,SRR25917833,SRX21637666,SRS18807755,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02942,GSM7761839,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02942,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6,GSM7761839,GSM7761839: 22 02942; Danio rerio; RNA Seq,GSM7761839 r1,GSM7761839,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02942_S16_L01_R1_001.fastq.gz 22-02942_S16_L01_R2_001.fastq.gz,fastq fastq,1924129256.0,9816986.0,GSM7761839 r1,0:98 1:98,A:513816169;C:444302395;G:442002444;T:522987233;N:1021015,98,98,,,513816169,444302395,442002444,522987233,1021015,SRX21637666,SRS18807755,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93541,0.9292,0.09209,0.09323,0.70496,0.70595,0.50865,0.51472,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26419,SRR25917834,SRX21637666,SRS18807755,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02942,GSM7761839,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02942,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6,GSM7761839,GSM7761839: 22 02942; Danio rerio; RNA Seq,GSM7761839 r1,GSM7761839,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02942_S16_L02_R1_001.fastq.gz 22-02942_S16_L02_R2_001.fastq.gz,fastq fastq,3006370892.0,15338627.0,GSM7761839 r2,0:98 1:98,A:798357725;C:699049238;G:696286354;T:812267336;N:410239,98,98,,,798357725,699049238,696286354,812267336,410239,SRX21637666,SRS18807755,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94371,0.93809,0.09,0.09081,0.70429,0.7054,0.50485,0.50657,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26420,SRR25917835,SRX21637666,SRS18807755,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02942,GSM7761839,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02942,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6,GSM7761839,GSM7761839: 22 02942; Danio rerio; RNA Seq,GSM7761839 r1,GSM7761839,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02942_S16_L03_R1_001.fastq.gz 22-02942_S16_L03_R2_001.fastq.gz,fastq fastq,2569908488.0,13111778.0,GSM7761839 r3,0:98 1:98,A:683489191;C:595497651;G:593400486;T:696913366;N:607794,98,98,,,683489191,595497651,593400486,696913366,607794,SRX21637666,SRS18807755,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94243,0.93803,0.0901,0.09173,0.70601,0.70595,0.5082,0.50536,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26421,SRR25917836,SRX21637666,SRS18807755,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02942,GSM7761839,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02942,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6,GSM7761839,GSM7761839: 22 02942; Danio rerio; RNA Seq,GSM7761839 r1,GSM7761839,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02942_S16_L04_R1_001.fastq.gz 22-02942_S16_L04_R2_001.fastq.gz,fastq fastq,4090784012.0,20871347.0,GSM7761839 r4,0:98 1:98,A:1082885031;C:953380881;G:951809866;T:1102604651;N:103583,98,98,,,1082885031,953380881,951809866,1102604651,103583,SRX21637666,SRS18807755,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9483,0.94389,0.08825,0.08951,0.70575,0.70642,0.5123,0.50956,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26422,SRR25917837,SRX21637665,SRS18807754,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02941,GSM7761838,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02941,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6,GSM7761838,GSM7761838: 22 02941; Danio rerio; RNA Seq,GSM7761838 r1,GSM7761838,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02941_S15_L01_R1_001.fastq.gz 22-02941_S15_L01_R2_001.fastq.gz,fastq fastq,1451986424.0,7408094.0,GSM7761838 r1,0:98 1:98,A:390918596;C:332118752;G:330611037;T:397580767;N:757272,98,98,,,390918596,332118752,330611037,397580767,757272,SRX21637665,SRS18807754,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93162,0.92627,0.10255,0.10375,0.7067,0.70741,0.48748,0.50266,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26423,SRR25917838,SRX21637665,SRS18807754,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02941,GSM7761838,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02941,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6,GSM7761838,GSM7761838: 22 02941; Danio rerio; RNA Seq,GSM7761838 r1,GSM7761838,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02941_S15_L02_R1_001.fastq.gz 22-02941_S15_L02_R2_001.fastq.gz,fastq fastq,2226903784.0,11361754.0,GSM7761838 r2,0:98 1:98,A:595644295;C:513538924;G:511376888;T:606030075;N:313602,98,98,,,595644295,513538924,511376888,606030075,313602,SRX21637665,SRS18807754,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94004,0.93541,0.09921,0.10033,0.70374,0.70471,0.50851,0.50748,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26424,SRR25917839,SRX21637665,SRS18807754,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02941,GSM7761838,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02941,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6,GSM7761838,GSM7761838: 22 02941; Danio rerio; RNA Seq,GSM7761838 r1,GSM7761838,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02941_S15_L03_R1_001.fastq.gz 22-02941_S15_L03_R2_001.fastq.gz,fastq fastq,1835563128.0,9365118.0,GSM7761838 r3,0:98 1:98,A:491600256;C:421963198;G:420470403;T:501084604;N:444667,98,98,,,491600256,421963198,420470403,501084604,444667,SRX21637665,SRS18807754,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93909,0.93552,0.09787,0.10025,0.7063,0.70668,0.49667,0.49612,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26425,SRR25917840,SRX21637665,SRS18807754,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02941,GSM7761838,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing,22 02941,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6,GSM7761838,GSM7761838: 22 02941; Danio rerio; RNA Seq,GSM7761838 r1,GSM7761838,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02941_S15_L04_R1_001.fastq.gz 22-02941_S15_L04_R2_001.fastq.gz,fastq fastq,3014378668.0,15379483.0,GSM7761838 r4,0:98 1:98,A:802870126;C:697333543;G:696291116;T:817807708;N:76175,98,98,,,802870126,697333543,696291116,817807708,76175,SRX21637665,SRS18807754,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94458,0.94088,0.0997,0.10084,0.70542,0.70615,0.49847,0.50128,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26426,SRR25917841,SRX21637664,SRS18807753,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02938,GSM7761837,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing,22 02938,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2,GSM7761837,GSM7761837: 22 02938; Danio rerio; RNA Seq,GSM7761837 r1,GSM7761837,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02938_S14_L01_R1_001.fastq.gz 22-02938_S14_L01_R2_001.fastq.gz,fastq fastq,1991261020.0,10159495.0,GSM7761837 r1,0:98 1:98,A:532249087;C:459160151;G:456558143;T:542243720;N:1049919,98,98,,,532249087,459160151,456558143,542243720,1049919,SRX21637664,SRS18807753,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93301,0.92619,0.10156,0.10145,0.70203,0.70354,0.50217,0.50319,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26427,SRR25917842,SRX21637664,SRS18807753,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02938,GSM7761837,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing,22 02938,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2,GSM7761837,GSM7761837: 22 02938; Danio rerio; RNA Seq,GSM7761837 r1,GSM7761837,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02938_S14_L02_R1_001.fastq.gz 22-02938_S14_L02_R2_001.fastq.gz,fastq fastq,3089219896.0,15761326.0,GSM7761837 r2,0:98 1:98,A:820946080;C:717486845;G:714242053;T:836115769;N:429149,98,98,,,820946080,717486845,714242053,836115769,429149,SRX21637664,SRS18807753,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93958,0.93485,0.09922,0.10087,0.70297,0.70374,0.48594,0.48787,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26428,SRR25917843,SRX21637664,SRS18807753,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02938,GSM7761837,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing,22 02938,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2,GSM7761837,GSM7761837: 22 02938; Danio rerio; RNA Seq,GSM7761837 r1,GSM7761837,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02938_S14_L03_R1_001.fastq.gz 22-02938_S14_L03_R2_001.fastq.gz,fastq fastq,2646575652.0,13502937.0,GSM7761837 r3,0:98 1:98,A:704124909;C:612713176;G:610276201;T:718835355;N:626011,98,98,,,704124909,612713176,610276201,718835355,626011,SRX21637664,SRS18807753,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93984,0.93514,0.09825,0.09978,0.70368,0.70364,0.50476,0.5062,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26429,SRR25917844,SRX21637664,SRS18807753,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02938,GSM7761837,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing,22 02938,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2,GSM7761837,GSM7761837: 22 02938; Danio rerio; RNA Seq,GSM7761837 r1,GSM7761837,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02938_S14_L04_R1_001.fastq.gz 22-02938_S14_L04_R2_001.fastq.gz,fastq fastq,4235942788.0,21611953.0,GSM7761837 r4,0:98 1:98,A:1121922192;C:986087720;G:984166129;T:1143659828;N:106919,98,98,,,1121922192,986087720,984166129,1143659828,106919,SRX21637664,SRS18807753,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94454,0.94039,0.09757,0.09901,0.70035,0.70138,0.49729,0.48826,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26430,SRR25917845,SRX21637663,SRS18807752,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02937,GSM7761836,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing,22 02937,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3,GSM7761836,GSM7761836: 22 02937; Danio rerio; RNA Seq,GSM7761836 r1,GSM7761836,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02937_S13_L01_R1_001.fastq.gz 22-02937_S13_L01_R2_001.fastq.gz,fastq fastq,1825781944.0,9315214.0,GSM7761836 r1,0:98 1:98,A:489329069;C:419397972;G:418043678;T:498054837;N:956388,98,98,,,489329069,419397972,418043678,498054837,956388,SRX21637663,SRS18807752,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93216,0.9269,0.10415,0.10514,0.70696,0.70713,0.50133,0.50188,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26431,SRR25917846,SRX21637663,SRS18807752,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02937,GSM7761836,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing,22 02937,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3,GSM7761836,GSM7761836: 22 02937; Danio rerio; RNA Seq,GSM7761836 r1,GSM7761836,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02937_S13_L02_R1_001.fastq.gz 22-02937_S13_L02_R2_001.fastq.gz,fastq fastq,2831655708.0,14447223.0,GSM7761836 r2,0:98 1:98,A:753926233;C:655777502;G:654115498;T:767448178;N:388297,98,98,,,753926233,655777502,654115498,767448178,388297,SRX21637663,SRS18807752,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93913,0.93449,0.10226,0.10403,0.70623,0.70698,0.50808,0.5015,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26432,SRR25917847,SRX21637663,SRS18807752,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02937,GSM7761836,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing,22 02937,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3,GSM7761836,GSM7761836: 22 02937; Danio rerio; RNA Seq,GSM7761836 r1,GSM7761836,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02937_S13_L03_R1_001.fastq.gz 22-02937_S13_L03_R2_001.fastq.gz,fastq fastq,2309829816.0,11784846.0,GSM7761836 r3,0:98 1:98,A:615504790;C:533456596;G:532490021;T:627819856;N:558553,98,98,,,615504790,533456596,532490021,627819856,558553,SRX21637663,SRS18807752,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93883,0.93641,0.10187,0.10383,0.70615,0.70593,0.49921,0.49159,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26433,SRR25917848,SRX21637663,SRS18807752,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02937,GSM7761836,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing,22 02937,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3,GSM7761836,GSM7761836: 22 02937; Danio rerio; RNA Seq,GSM7761836 r1,GSM7761836,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02937_S13_L04_R1_001.fastq.gz 22-02937_S13_L04_R2_001.fastq.gz,fastq fastq,3731146944.0,19036464.0,GSM7761836 r4,0:98 1:98,A:989277206;C:866724233;G:866705291;T:1008347419;N:92795,98,98,,,989277206,866724233,866705291,1008347419,92795,SRX21637663,SRS18807752,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9451,0.94176,0.10033,0.10187,0.70494,0.70571,0.49807,0.49112,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26434,SRR25917849,SRX21637662,SRS18807751,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02936,GSM7761835,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02936,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761835,GSM7761835: 22 02936; Danio rerio; RNA Seq,GSM7761835 r1,GSM7761835,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02936_S12_L01_R1_001.fastq.gz 22-02936_S12_L01_R2_001.fastq.gz,fastq fastq,2087585416.0,10650946.0,GSM7761835 r1,0:98 1:98,A:557206023;C:482369335;G:479442541;T:567486868;N:1080649,98,98,,,557206023,482369335,479442541,567486868,1080649,SRX21637662,SRS18807751,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93131,0.92508,0.10425,0.10495,0.70715,0.70796,0.49956,0.48457,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26435,SRR25917850,SRX21637662,SRS18807751,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02936,GSM7761835,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02936,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761835,GSM7761835: 22 02936; Danio rerio; RNA Seq,GSM7761835 r1,GSM7761835,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02936_S12_L02_R1_001.fastq.gz 22-02936_S12_L02_R2_001.fastq.gz,fastq fastq,3225005756.0,16454111.0,GSM7761835 r2,0:98 1:98,A:855605850;C:750757069;G:747157352;T:871043603;N:441882,98,98,,,855605850,750757069,747157352,871043603,441882,SRX21637662,SRS18807751,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93771,0.93339,0.10257,0.10429,0.70601,0.70727,0.50591,0.50179,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26436,SRR25917851,SRX21637662,SRS18807751,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02936,GSM7761835,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02936,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761835,GSM7761835: 22 02936; Danio rerio; RNA Seq,GSM7761835 r1,GSM7761835,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02936_S12_L03_R1_001.fastq.gz 22-02936_S12_L03_R2_001.fastq.gz,fastq fastq,2793582512.0,14252972.0,GSM7761835 r3,0:98 1:98,A:742243213;C:648028314;G:645258591;T:757391700;N:660694,98,98,,,742243213,648028314,645258591,757391700,660694,SRX21637662,SRS18807751,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9379,0.9345,0.10089,0.10292,0.70887,0.70907,0.48756,0.50559,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26437,SRR25917852,SRX21637662,SRS18807751,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02936,GSM7761835,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing,22 02936,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5,GSM7761835,GSM7761835: 22 02936; Danio rerio; RNA Seq,GSM7761835 r1,GSM7761835,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02936_S12_L04_R1_001.fastq.gz 22-02936_S12_L04_R2_001.fastq.gz,fastq fastq,4412090144.0,22510664.0,GSM7761835 r4,0:98 1:98,A:1166366926;C:1029504824;G:1027522438;T:1188583356;N:112600,98,98,,,1166366926,1029504824,1027522438,1188583356,112600,SRX21637662,SRS18807751,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9434,0.94005,0.10109,0.10212,0.70565,0.70627,0.49953,0.49393,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26438,SRR25917853,SRX21637661,SRS18807750,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02935,GSM7761834,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing,22 02935,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3,GSM7761834,GSM7761834: 22 02935; Danio rerio; RNA Seq,GSM7761834 r1,GSM7761834,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02935_S11_L01_R1_001.fastq.gz 22-02935_S11_L01_R2_001.fastq.gz,fastq fastq,1425260256.0,7271736.0,GSM7761834 r1,0:98 1:98,A:380769821;C:328986720;G:327546654;T:387200001;N:757060,98,98,,,380769821,328986720,327546654,387200001,757060,SRX21637661,SRS18807750,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93263,0.92464,0.09384,0.0946,0.70145,0.70159,0.50261,0.49541,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26439,SRR25917854,SRX21637661,SRS18807750,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02935,GSM7761834,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing,22 02935,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3,GSM7761834,GSM7761834: 22 02935; Danio rerio; RNA Seq,GSM7761834 r1,GSM7761834,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02935_S11_L02_R1_001.fastq.gz 22-02935_S11_L02_R2_001.fastq.gz,fastq fastq,2182395712.0,11134672.0,GSM7761834 r2,0:98 1:98,A:579577501;C:507352278;G:505817817;T:589350119;N:297997,98,98,,,579577501,507352278,505817817,589350119,297997,SRX21637661,SRS18807750,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94061,0.93492,0.09299,0.09327,0.69968,0.69972,0.50173,0.50685,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26440,SRR25917855,SRX21637661,SRS18807750,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02935,GSM7761834,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing,22 02935,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3,GSM7761834,GSM7761834: 22 02935; Danio rerio; RNA Seq,GSM7761834 r1,GSM7761834,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02935_S11_L03_R1_001.fastq.gz 22-02935_S11_L03_R2_001.fastq.gz,fastq fastq,1865940776.0,9520106.0,GSM7761834 r3,0:98 1:98,A:496030337;C:432591349;G:431482394;T:505389204;N:447492,98,98,,,496030337,432591349,431482394,505389204,447492,SRX21637661,SRS18807750,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93989,0.93593,0.09052,0.09217,0.70364,0.70408,0.49553,0.50339,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26441,SRR25917856,SRX21637661,SRS18807750,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02935,GSM7761834,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing,22 02935,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3,GSM7761834,GSM7761834: 22 02935; Danio rerio; RNA Seq,GSM7761834 r1,GSM7761834,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02935_S11_L04_R1_001.fastq.gz 22-02935_S11_L04_R2_001.fastq.gz,fastq fastq,2911163500.0,14852875.0,GSM7761834 r4,0:98 1:98,A:770358038;C:678412695;G:678127449;T:784190944;N:74374,98,98,,,770358038,678412695,678127449,784190944,74374,SRX21637661,SRS18807750,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9457,0.94244,0.0911,0.09245,0.70118,0.70242,0.50638,0.51106,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26442,SRR25917857,SRX21637660,SRS18807749,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02934,GSM7761833,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02934,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761833,GSM7761833: 22 02934; Danio rerio; RNA Seq,GSM7761833 r1,GSM7761833,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02934_S10_L01_R1_001.fastq.gz 22-02934_S10_L01_R2_001.fastq.gz,fastq fastq,1634748192.0,8340552.0,GSM7761833 r1,0:98 1:98,A:437596034;C:376561669;G:375555537;T:444177229;N:857723,98,98,,,437596034,376561669,375555537,444177229,857723,SRX21637660,SRS18807749,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93351,0.93037,0.09754,0.09921,0.70386,0.70441,0.50777,0.50601,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26443,SRR25917858,SRX21637660,SRS18807749,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02934,GSM7761833,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02934,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761833,GSM7761833: 22 02934; Danio rerio; RNA Seq,GSM7761833 r1,GSM7761833,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02934_S10_L02_R1_001.fastq.gz 22-02934_S10_L02_R2_001.fastq.gz,fastq fastq,2555331184.0,13037404.0,GSM7761833 r2,0:98 1:98,A:679972731;C:592870022;G:591661544;T:690487300;N:339587,98,98,,,679972731,592870022,591661544,690487300,339587,SRX21637660,SRS18807749,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94259,0.93773,0.09654,0.09727,0.70276,0.7036,0.51546,0.51595,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26444,SRR25917859,SRX21637660,SRS18807749,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02934,GSM7761833,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02934,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761833,GSM7761833: 22 02934; Danio rerio; RNA Seq,GSM7761833 r1,GSM7761833,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02934_S10_L03_R1_001.fastq.gz 22-02934_S10_L03_R2_001.fastq.gz,fastq fastq,2126669188.0,10850353.0,GSM7761833 r3,0:98 1:98,A:566657230;C:491844144;G:491125243;T:576536074;N:506497,98,98,,,566657230,491844144,491125243,576536074,506497,SRX21637660,SRS18807749,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94132,0.93954,0.09627,0.09813,0.70141,0.70207,0.50833,0.50945,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26445,SRR25917860,SRX21637660,SRS18807749,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02934,GSM7761833,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02934,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761833,GSM7761833: 22 02934; Danio rerio; RNA Seq,GSM7761833 r1,GSM7761833,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02934_S10_L04_R1_001.fastq.gz 22-02934_S10_L04_R2_001.fastq.gz,fastq fastq,3389559320.0,17293670.0,GSM7761833 r4,0:98 1:98,A:899016289;C:788251756;G:788352656;T:913853588;N:85031,98,98,,,899016289,788251756,788352656,913853588,85031,SRX21637660,SRS18807749,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94631,0.94381,0.09528,0.0969,0.7027,0.70297,0.50668,0.51126,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26446,SRR25917861,SRX21637659,SRS18807748,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02933,GSM7761832,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing,22 02933,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9,GSM7761832,GSM7761832: 22 02933; Danio rerio; RNA Seq,GSM7761832 r1,GSM7761832,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02933_S9_L01_R1_001.fastq.gz 22-02933_S9_L01_R2_001.fastq.gz,fastq fastq,1625039920.0,8291020.0,GSM7761832 r1,0:98 1:98,A:437446017;C:372483047;G:371043665;T:443213897;N:853294,98,98,,,437446017,372483047,371043665,443213897,853294,SRX21637659,SRS18807748,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.92998,0.92392,0.10748,0.10946,0.70836,0.70847,0.48907,0.48857,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26447,SRR25917862,SRX21637659,SRS18807748,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02933,GSM7761832,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing,22 02933,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9,GSM7761832,GSM7761832: 22 02933; Danio rerio; RNA Seq,GSM7761832 r1,GSM7761832,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02933_S9_L02_R1_001.fastq.gz 22-02933_S9_L02_R2_001.fastq.gz,fastq fastq,2511173364.0,12812109.0,GSM7761832 r2,0:98 1:98,A:671571720;C:580389475;G:578546462;T:680316728;N:348979,98,98,,,671571720,580389475,578546462,680316728,348979,SRX21637659,SRS18807748,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93833,0.93295,0.10554,0.10659,0.70694,0.70725,0.49015,0.48342,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26448,SRR25917863,SRX21637659,SRS18807748,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02933,GSM7761832,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing,22 02933,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9,GSM7761832,GSM7761832: 22 02933; Danio rerio; RNA Seq,GSM7761832 r1,GSM7761832,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02933_S9_L03_R1_001.fastq.gz 22-02933_S9_L03_R2_001.fastq.gz,fastq fastq,2142414064.0,10930684.0,GSM7761832 r3,0:98 1:98,A:573997088;C:493219654;G:491924100;T:582757555;N:515667,98,98,,,573997088,493219654,491924100,582757555,515667,SRX21637659,SRS18807748,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93772,0.93308,0.10567,0.10721,0.70741,0.70802,0.49025,0.49086,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26449,SRR25917864,SRX21637659,SRS18807748,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02933,GSM7761832,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing,22 02933,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9,GSM7761832,GSM7761832: 22 02933; Danio rerio; RNA Seq,GSM7761832 r1,GSM7761832,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02933_S9_L04_R1_001.fastq.gz 22-02933_S9_L04_R2_001.fastq.gz,fastq fastq,3407370232.0,17384542.0,GSM7761832 r4,0:98 1:98,A:907918258;C:789555234;G:788822588;T:920987647;N:86505,98,98,,,907918258,789555234,788822588,920987647,86505,SRX21637659,SRS18807748,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9434,0.93934,0.10586,0.10664,0.70597,0.7064,0.49476,0.49501,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26450,SRR25917865,SRX21637658,SRS18807747,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02932,GSM7761831,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing,22 02932,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3,GSM7761831,GSM7761831: 22 02932; Danio rerio; RNA Seq,GSM7761831 r1,GSM7761831,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02932_S8_L01_R1_001.fastq.gz 22-02932_S8_L01_R2_001.fastq.gz,fastq fastq,1652834484.0,8432829.0,GSM7761831 r1,0:98 1:98,A:445714221;C:377297450;G:376171010;T:452774158;N:877645,98,98,,,445714221,377297450,376171010,452774158,877645,SRX21637658,SRS18807747,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.92783,0.92405,0.11309,0.11435,0.70502,0.70516,0.51245,0.51191,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26451,SRR25917866,SRX21637658,SRS18807747,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02932,GSM7761831,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing,22 02932,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3,GSM7761831,GSM7761831: 22 02932; Danio rerio; RNA Seq,GSM7761831 r1,GSM7761831,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02932_S8_L02_R1_001.fastq.gz 22-02932_S8_L02_R2_001.fastq.gz,fastq fastq,2483826268.0,12672583.0,GSM7761831 r2,0:98 1:98,A:666132559;C:571071547;G:570172380;T:676097026;N:352756,98,98,,,666132559,571071547,570172380,676097026,352756,SRX21637658,SRS18807747,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9372,0.93314,0.1107,0.11198,0.7024,0.70311,0.50775,0.49851,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26452,SRR25917867,SRX21637658,SRS18807747,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02932,GSM7761831,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing,22 02932,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3,GSM7761831,GSM7761831: 22 02932; Danio rerio; RNA Seq,GSM7761831 r1,GSM7761831,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02932_S8_L03_R1_001.fastq.gz 22-02932_S8_L03_R2_001.fastq.gz,fastq fastq,2257194408.0,11516298.0,GSM7761831 r3,0:98 1:98,A:605680300;C:517703393;G:517093157;T:616181689;N:535869,98,98,,,605680300,517703393,517093157,616181689,535869,SRX21637658,SRS18807747,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93599,0.9327,0.10967,0.11188,0.70421,0.70485,0.50619,0.50505,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26453,SRR25917868,SRX21637658,SRS18807747,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02932,GSM7761831,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing,22 02932,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3,GSM7761831,GSM7761831: 22 02932; Danio rerio; RNA Seq,GSM7761831 r1,GSM7761831,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02932_S8_L04_R1_001.fastq.gz 22-02932_S8_L04_R2_001.fastq.gz,fastq fastq,3522571388.0,17972303.0,GSM7761831 r4,0:98 1:98,A:941638147;C:811658683;G:812442792;T:956741032;N:90734,98,98,,,941638147,811658683,812442792,956741032,90734,SRX21637658,SRS18807747,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94177,0.93937,0.11052,0.11233,0.70094,0.70185,0.50644,0.50654,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26454,SRR25917869,SRX21637657,SRS18807746,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02931,GSM7761830,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02931,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761830,GSM7761830: 22 02931; Danio rerio; RNA Seq,GSM7761830 r1,GSM7761830,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02931_S7_L01_R1_001.fastq.gz 22-02931_S7_L01_R2_001.fastq.gz,fastq fastq,2078034924.0,10602219.0,GSM7761830 r1,0:98 1:98,A:556960818;C:477871614;G:476758987;T:565357168;N:1086337,98,98,,,556960818,477871614,476758987,565357168,1086337,SRX21637657,SRS18807746,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93055,0.92614,0.10155,0.10219,0.70238,0.70285,0.49809,0.49641,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26455,SRR25917870,SRX21637657,SRS18807746,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02931,GSM7761830,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02931,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761830,GSM7761830: 22 02931; Danio rerio; RNA Seq,GSM7761830 r1,GSM7761830,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02931_S7_L02_R1_001.fastq.gz 22-02931_S7_L02_R2_001.fastq.gz,fastq fastq,3163234592.0,16138952.0,GSM7761830 r2,0:98 1:98,A:842478174;C:733095294;G:732049286;T:855168777;N:443061,98,98,,,842478174,733095294,732049286,855168777,443061,SRX21637657,SRS18807746,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93831,0.93463,0.10061,0.10137,0.70276,0.70362,0.48735,0.49231,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26456,SRR25917871,SRX21637657,SRS18807746,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02931,GSM7761830,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02931,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761830,GSM7761830: 22 02931; Danio rerio; RNA Seq,GSM7761830 r1,GSM7761830,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02931_S7_L03_R1_001.fastq.gz 22-02931_S7_L03_R2_001.fastq.gz,fastq fastq,2674741832.0,13646642.0,GSM7761830 r3,0:98 1:98,A:712547758;C:618664398;G:618024646;T:724874022;N:631008,98,98,,,712547758,618664398,618024646,724874022,631008,SRX21637657,SRS18807746,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93914,0.93649,0.09901,0.10101,0.70329,0.70309,0.49131,0.48443,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26457,SRR25917872,SRX21637657,SRS18807746,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02931,GSM7761830,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing,22 02931,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1,GSM7761830,GSM7761830: 22 02931; Danio rerio; RNA Seq,GSM7761830 r1,GSM7761830,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02931_S7_L04_R1_001.fastq.gz 22-02931_S7_L04_R2_001.fastq.gz,fastq fastq,4163977076.0,21244781.0,GSM7761830 r4,0:98 1:98,A:1104518063;C:967955798;G:968931822;T:1122465534;N:105859,98,98,,,1104518063,967955798,968931822,1122465534,105859,SRX21637657,SRS18807746,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94358,0.94145,0.09856,0.0999,0.7022,0.7023,0.49231,0.49411,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26458,SRR25917873,SRX21637656,SRS18807745,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02930,GSM7761829,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02930,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5,GSM7761829,GSM7761829: 22 02930; Danio rerio; RNA Seq,GSM7761829 r1,GSM7761829,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02930_S6_L01_R1_001.fastq.gz 22-02930_S6_L01_R2_001.fastq.gz,fastq fastq,2183053488.0,11138028.0,GSM7761829 r1,0:98 1:98,A:587746222;C:499739594;G:498918963;T:595474490;N:1174219,98,98,,,587746222,499739594,498918963,595474490,1174219,SRX21637656,SRS18807745,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93008,0.92301,0.10276,0.10349,0.70467,0.70477,0.50182,0.4904,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26459,SRR25917874,SRX21637656,SRS18807745,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02930,GSM7761829,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02930,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5,GSM7761829,GSM7761829: 22 02930; Danio rerio; RNA Seq,GSM7761829 r1,GSM7761829,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02930_S6_L02_R1_001.fastq.gz 22-02930_S6_L02_R2_001.fastq.gz,fastq fastq,3272267236.0,16695241.0,GSM7761829 r2,0:98 1:98,A:875782986;C:754682745;G:754270029;T:887061936;N:469540,98,98,,,875782986,754682745,754270029,887061936,469540,SRX21637656,SRS18807745,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93964,0.93399,0.10278,0.10253,0.70272,0.70356,0.50742,0.50718,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26460,SRR25917875,SRX21637656,SRS18807745,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02930,GSM7761829,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02930,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5,GSM7761829,GSM7761829: 22 02930; Danio rerio; RNA Seq,GSM7761829 r1,GSM7761829,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02930_S6_L03_R1_001.fastq.gz 22-02930_S6_L03_R2_001.fastq.gz,fastq fastq,2933063560.0,14964610.0,GSM7761829 r3,0:98 1:98,A:785485812;C:674759421;G:674660900;T:797470873;N:686554,98,98,,,785485812,674759421,674660900,797470873,686554,SRX21637656,SRS18807745,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93883,0.93435,0.09945,0.10079,0.70394,0.70412,0.49002,0.5013,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26461,SRR25917876,SRX21637656,SRS18807745,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02930,GSM7761829,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing,22 02930,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5,GSM7761829,GSM7761829: 22 02930; Danio rerio; RNA Seq,GSM7761829 r1,GSM7761829,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02930_S6_L04_R1_001.fastq.gz 22-02930_S6_L04_R2_001.fastq.gz,fastq fastq,4750945136.0,24239516.0,GSM7761829 r4,0:98 1:98,A:1268488476;C:1097018233;G:1099272584;T:1286042389;N:123454,98,98,,,1268488476,1097018233,1099272584,1286042389,123454,SRX21637656,SRS18807745,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94232,0.93878,0.09951,0.10061,0.70327,0.70516,0.50625,0.50124,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26462,SRR25917877,SRX21637655,SRS18807744,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02929,GSM7761828,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing,22 02929,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1,GSM7761828,GSM7761828: 22 02929; Danio rerio; RNA Seq,GSM7761828 r1,GSM7761828,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02929_S5_L01_R1_001.fastq.gz 22-02929_S5_L01_R2_001.fastq.gz,fastq fastq,1624362544.0,8287564.0,GSM7761828 r1,0:98 1:98,A:436056094;C:372956179;G:372275222;T:442210214;N:864835,98,98,,,436056094,372956179,372275222,442210214,864835,SRX21637655,SRS18807744,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93013,0.92347,0.1043,0.10462,0.70439,0.70496,0.48768,0.48699,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26463,SRR25917878,SRX21637655,SRS18807744,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02929,GSM7761828,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing,22 02929,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1,GSM7761828,GSM7761828: 22 02929; Danio rerio; RNA Seq,GSM7761828 r1,GSM7761828,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02929_S5_L02_R1_001.fastq.gz 22-02929_S5_L02_R2_001.fastq.gz,fastq fastq,2437979712.0,12438672.0,GSM7761828 r2,0:98 1:98,A:650251653;C:564250362;G:563686737;T:659443371;N:347589,98,98,,,650251653,564250362,563686737,659443371,347589,SRX21637655,SRS18807744,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93808,0.93228,0.10217,0.10348,0.7052,0.70642,0.48354,0.49828,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26464,SRR25917879,SRX21637655,SRS18807744,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02929,GSM7761828,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing,22 02929,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1,GSM7761828,GSM7761828: 22 02929; Danio rerio; RNA Seq,GSM7761828 r1,GSM7761828,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02929_S5_L03_R1_001.fastq.gz 22-02929_S5_L03_R2_001.fastq.gz,fastq fastq,2103094896.0,10730076.0,GSM7761828 r3,0:98 1:98,A:561587272;C:485245220;G:484987810;T:570768889;N:505705,98,98,,,561587272,485245220,484987810,570768889,505705,SRX21637655,SRS18807744,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9374,0.93318,0.10153,0.1033,0.70283,0.70274,0.49345,0.49097,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26465,SRR25917880,SRX21637655,SRS18807744,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02929,GSM7761828,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing,22 02929,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1,GSM7761828,GSM7761828: 22 02929; Danio rerio; RNA Seq,GSM7761828 r1,GSM7761828,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02929_S5_L04_R1_001.fastq.gz 22-02929_S5_L04_R2_001.fastq.gz,fastq fastq,3339247884.0,17036979.0,GSM7761828 r4,0:98 1:98,A:887185623;C:774852471;G:776222517;T:900901929;N:85344,98,98,,,887185623,774852471,776222517,900901929,85344,SRX21637655,SRS18807744,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94331,0.93927,0.1008,0.10184,0.70124,0.70116,0.49593,0.48864,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26466,SRR25917881,SRX21637654,SRS18807743,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02928,GSM7761827,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing,22 02928,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3,GSM7761827,GSM7761827: 22 02928; Danio rerio; RNA Seq,GSM7761827 r1,GSM7761827,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02928_S4_L01_R1_001.fastq.gz 22-02928_S4_L01_R2_001.fastq.gz,fastq fastq,1820089908.0,9286173.0,GSM7761827 r1,0:98 1:98,A:489328752;C:417340608;G:416061821;T:496389968;N:968759,98,98,,,489328752,417340608,416061821,496389968,968759,SRX21637654,SRS18807743,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93058,0.92445,0.10789,0.10868,0.70311,0.70437,0.49514,0.49715,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26467,SRR25917882,SRX21637654,SRS18807743,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02928,GSM7761827,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing,22 02928,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3,GSM7761827,GSM7761827: 22 02928; Danio rerio; RNA Seq,GSM7761827 r1,GSM7761827,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02928_S4_L02_R1_001.fastq.gz 22-02928_S4_L02_R2_001.fastq.gz,fastq fastq,2727217500.0,13914375.0,GSM7761827 r2,0:98 1:98,A:728407349;C:630438451;G:629147847;T:738834234;N:389619,98,98,,,728407349,630438451,629147847,738834234,389619,SRX21637654,SRS18807743,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93908,0.9332,0.10555,0.10608,0.70266,0.70374,0.5047,0.50096,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26468,SRR25917883,SRX21637654,SRS18807743,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02928,GSM7761827,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing,22 02928,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3,GSM7761827,GSM7761827: 22 02928; Danio rerio; RNA Seq,GSM7761827 r1,GSM7761827,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02928_S4_L03_R1_001.fastq.gz 22-02928_S4_L03_R2_001.fastq.gz,fastq fastq,2427694416.0,12386196.0,GSM7761827 r3,0:98 1:98,A:648902248;C:559681298;G:558831926;T:659701354;N:577590,98,98,,,648902248,559681298,558831926,659701354,577590,SRX21637654,SRS18807743,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93814,0.93483,0.10441,0.10596,0.7027,0.70262,0.49778,0.50481,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26469,SRR25917884,SRX21637654,SRS18807743,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02928,GSM7761827,,source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing,22 02928,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3,GSM7761827,GSM7761827: 22 02928; Danio rerio; RNA Seq,GSM7761827 r1,GSM7761827,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02928_S4_L04_R1_001.fastq.gz 22-02928_S4_L04_R2_001.fastq.gz,fastq fastq,3804812760.0,19412310.0,GSM7761827 r4,0:98 1:98,A:1013270293;C:880885167;G:881629294;T:1028929883;N:98123,98,98,,,1013270293,880885167,881629294,1028929883,98123,SRX21637654,SRS18807743,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94321,0.93986,0.10365,0.10474,0.70228,0.7023,0.50249,0.49514,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26470,SRR25917885,SRX21637653,SRS18807742,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02927,GSM7761826,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing,22 02927,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4,GSM7761826,GSM7761826: 22 02927; Danio rerio; RNA Seq,GSM7761826 r1,GSM7761826,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02927_S3_L01_R1_001.fastq.gz 22-02927_S3_L01_R2_001.fastq.gz,fastq fastq,2066568336.0,10543716.0,GSM7761826 r1,0:98 1:98,A:554968443;C:474349665;G:473384034;T:562774037;N:1092157,98,98,,,554968443,474349665,473384034,562774037,1092157,SRX21637653,SRS18807742,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.9305,0.92427,0.10545,0.10708,0.70445,0.70542,0.49546,0.49704,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26471,SRR25917886,SRX21637653,SRS18807742,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02927,GSM7761826,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing,22 02927,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4,GSM7761826,GSM7761826: 22 02927; Danio rerio; RNA Seq,GSM7761826 r1,GSM7761826,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02927_S3_L02_R1_001.fastq.gz 22-02927_S3_L02_R2_001.fastq.gz,fastq fastq,3133377324.0,15986619.0,GSM7761826 r2,0:98 1:98,A:836240845;C:724796464;G:723947563;T:847954984;N:437468,98,98,,,836240845,724796464,723947563,847954984,437468,SRX21637653,SRS18807742,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93854,0.93416,0.1047,0.1054,0.7026,0.70325,0.50612,0.49753,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26472,SRR25917887,SRX21637653,SRS18807742,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02927,GSM7761826,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing,22 02927,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4,GSM7761826,GSM7761826: 22 02927; Danio rerio; RNA Seq,GSM7761826 r1,GSM7761826,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02927_S3_L03_R1_001.fastq.gz 22-02927_S3_L03_R2_001.fastq.gz,fastq fastq,2712126480.0,13837380.0,GSM7761826 r3,0:98 1:98,A:724693867;C:625398498;G:624928471;T:736458337;N:647307,98,98,,,724693867,625398498,624928471,736458337,647307,SRX21637653,SRS18807742,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93801,0.93409,0.1026,0.10389,0.70437,0.70362,0.49241,0.4932,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26473,SRR25917888,SRX21637653,SRS18807742,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02927,GSM7761826,,source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing,22 02927,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4,GSM7761826,GSM7761826: 22 02927; Danio rerio; RNA Seq,GSM7761826 r1,GSM7761826,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02927_S3_L04_R1_001.fastq.gz 22-02927_S3_L04_R2_001.fastq.gz,fastq fastq,4313396892.0,22007127.0,GSM7761826 r4,0:98 1:98,A:1147167739;C:999728613;G:1001587767;T:1164801430;N:111343,98,98,,,1147167739,999728613,1001587767,1164801430,111343,SRX21637653,SRS18807742,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94284,0.94033,0.10365,0.10505,0.70372,0.70502,0.50217,0.50133,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26474,SRR25917889,SRX21637652,SRS18807741,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02925,GSM7761825,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing,22 02925,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7,GSM7761825,GSM7761825: 22 02925; Danio rerio; RNA Seq,GSM7761825 r1,GSM7761825,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02925_S2_L01_R1_001.fastq.gz 22-02925_S2_L01_R2_001.fastq.gz,fastq fastq,1648026212.0,8408297.0,GSM7761825 r1,0:98 1:98,A:446399368;C:374586860;G:374491332;T:451683865;N:864787,98,98,,,446399368,374586860,374491332,451683865,864787,SRX21637652,SRS18807741,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.92802,0.92032,0.11753,0.11787,0.7021,0.70187,0.49703,0.49712,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26475,SRR25917890,SRX21637652,SRS18807741,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02925,GSM7761825,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing,22 02925,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7,GSM7761825,GSM7761825: 22 02925; Danio rerio; RNA Seq,GSM7761825 r1,GSM7761825,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02925_S2_L02_R1_001.fastq.gz 22-02925_S2_L02_R2_001.fastq.gz,fastq fastq,2515102380.0,12832155.0,GSM7761825 r2,0:98 1:98,A:677045156;C:576190894;G:576470691;T:685037037;N:358602,98,98,,,677045156,576190894,576470691,685037037,358602,SRX21637652,SRS18807741,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93607,0.93068,0.1164,0.11733,0.69962,0.70055,0.48548,0.48955,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26476,SRR25917891,SRX21637652,SRS18807741,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02925,GSM7761825,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing,22 02925,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7,GSM7761825,GSM7761825: 22 02925; Danio rerio; RNA Seq,GSM7761825 r1,GSM7761825,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02925_S2_L03_R1_001.fastq.gz 22-02925_S2_L03_R2_001.fastq.gz,fastq fastq,2154179160.0,10990710.0,GSM7761825 r3,0:98 1:98,A:580018273;C:492429243;G:492990917;T:588225663;N:515064,98,98,,,580018273,492429243,492990917,588225663,515064,SRX21637652,SRS18807741,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93587,0.93118,0.11365,0.11579,0.7023,0.70329,0.49574,0.48903,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26477,SRR25917892,SRX21637652,SRS18807741,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02925,GSM7761825,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing,22 02925,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7,GSM7761825,GSM7761825: 22 02925; Danio rerio; RNA Seq,GSM7761825 r1,GSM7761825,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02925_S2_L04_R1_001.fastq.gz 22-02925_S2_L04_R2_001.fastq.gz,fastq fastq,3442755288.0,17565078.0,GSM7761825 r4,0:98 1:98,A:922795011;C:791376920;G:793569039;T:934926963;N:87355,98,98,,,922795011,791376920,793569039,934926963,87355,SRX21637652,SRS18807741,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94191,0.93808,0.1144,0.11572,0.69988,0.69992,0.49539,0.49607,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26478,SRR25917893,SRX21637651,SRS18807740,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02924,GSM7761824,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:2|rin:8.7|geo loc name:missing|collection date:missing,22 02924,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:2|rin:8.7,GSM7761824,GSM7761824: 22 02924; Danio rerio; RNA Seq,GSM7761824 r1,GSM7761824,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02924_S1_L01_R1_001.fastq.gz 22-02924_S1_L01_R2_001.fastq.gz,fastq fastq,1812771268.0,9248833.0,GSM7761824 r1,0:98 1:98,A:488778459;C:414245907;G:414681978;T:494109886;N:955038,98,98,,,488778459,414245907,414681978,494109886,955038,SRX21637651,SRS18807740,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.93157,0.925,0.10556,0.10667,0.70441,0.70516,0.49678,0.47929,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System
26479,SRR25917894,SRX21637651,SRS18807740,SRP458896,PRJNA1013345,Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome,GSE242370,Transcriptome Analysis,Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA,,,,22 02924,GSM7761824,,source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:2|rin:8.7|geo loc name:missing|collection date:missing,22 02924,fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts,whole brain,,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:2|rin:8.7,GSM7761824,GSM7761824: 22 02924; Danio rerio; RNA Seq,GSM7761824 r1,GSM7761824,1,RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP458896,,loader:fastq load.py,22-02924_S1_L02_R1_001.fastq.gz 22-02924_S1_L02_R2_001.fastq.gz,fastq fastq,2762531604.0,14094549.0,GSM7761824 r2,0:98 1:98,A:740219895;C:636156304;G:637302723;T:748457359;N:395323,98,98,,,740219895,636156304,637302723,748457359,395323,SRX21637651,SRS18807740,SRA1706756,The University of Adelaide,The University of Adelaide,2,0.94012,0.93368,0.10512,0.10532,0.70274,0.70325,0.5034,0.49161,98,98,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-09-05,Undetermined,Undetermined,Brain,Nervous System