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
24854,SRR25519420,SRX21249697,SRS18503946,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 TFA 4  3dpf,GSM7681266,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 TFA 4  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681266,GSM7681266: zebrafish  AR42 TFA 4  3dpf; Danio rerio; RNA Seq,GSM7681266 r1,GSM7681266,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz,fastq fastq,9896772900.0,32989243.0,GSM7681266 r1,0:150 1:150,A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0,150,150,,,2382403653,2457377213,2470646159,2586345875,0,SRX21249697,SRS18503946,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70537,0.88934,0.03159,0.04209,0.78013,0.75416,0.50713,0.45138,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24855,SRR25519421,SRX21249696,SRS18503945,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 TFA 3  3dpf,GSM7681265,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 TFA 3  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681265,GSM7681265: zebrafish  AR42 TFA 3  3dpf; Danio rerio; RNA Seq,GSM7681265 r1,GSM7681265,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz,fastq fastq,10265927100.0,34219757.0,GSM7681265 r1,0:150 1:150,A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0,150,150,,,2473552302,2548535087,2562873160,2680966551,0,SRX21249696,SRS18503945,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70516,0.88765,0.03163,0.04168,0.7782,0.75083,0.50851,0.45305,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24856,SRR25519422,SRX21249695,SRS18503944,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 TFA 2  3dpf,GSM7681264,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 TFA 2  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681264,GSM7681264: zebrafish  AR42 TFA 2  3dpf; Danio rerio; RNA Seq,GSM7681264 r1,GSM7681264,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz,fastq fastq,10003398900.0,33344663.0,GSM7681264 r1,0:150 1:150,A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0,150,150,,,2409580340,2483650756,2497057051,2613110753,0,SRX21249695,SRS18503944,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70787,0.89158,0.03203,0.04194,0.77851,0.75108,0.5072,0.45508,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24857,SRR25519423,SRX21249694,SRS18503943,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 TFA 1  3dpf,GSM7681263,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 TFA 1  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681263,GSM7681263: zebrafish  AR42 TFA 1  3dpf; Danio rerio; RNA Seq,GSM7681263 r1,GSM7681263,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz,fastq fastq,7420308900.0,24734363.0,GSM7681263 r1,0:150 1:150,A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0,150,150,,,1791092728,1841012408,1852583633,1935620131,0,SRX21249694,SRS18503943,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.69668,0.87862,0.03153,0.04215,0.77463,0.74949,0.50657,0.45971,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24858,SRR25519424,SRX21249693,SRS18503942,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO TFA 4  3dpf,GSM7681262,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO TFA 4  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681262,GSM7681262: zebrafish  DMSO TFA 4  3dpf; Danio rerio; RNA Seq,GSM7681262 r1,GSM7681262,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz,fastq fastq,10178474100.0,33928247.0,GSM7681262 r1,0:150 1:150,A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0,150,150,,,2452172460,2526571372,2532799116,2666931152,0,SRX21249693,SRS18503942,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.72132,0.91072,0.03161,0.04366,0.77709,0.75016,0.516,0.45312,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24859,SRR25519425,SRX21249692,SRS18503941,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO TFA 3  3dpf,GSM7681261,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO TFA 3  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681261,GSM7681261: zebrafish  DMSO TFA 3  3dpf; Danio rerio; RNA Seq,GSM7681261 r1,GSM7681261,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz,fastq fastq,9483201300.0,31610671.0,GSM7681261 r1,0:150 1:150,A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0,150,150,,,2282797855,2354211318,2361918927,2484273200,0,SRX21249692,SRS18503941,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71779,0.90757,0.03224,0.04329,0.77853,0.74862,0.51128,0.44891,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24860,SRR25519426,SRX21249691,SRS18503940,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO TFA 2  3dpf,GSM7681260,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO TFA 2  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681260,GSM7681260: zebrafish  DMSO TFA 2  3dpf; Danio rerio; RNA Seq,GSM7681260 r1,GSM7681260,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz,fastq fastq,9372641700.0,31242139.0,GSM7681260 r1,0:150 1:150,A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0,150,150,,,2255045813,2327185536,2333956274,2456454077,0,SRX21249691,SRS18503940,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71913,0.91061,0.0318,0.04251,0.7778,0.74907,0.51295,0.45006,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24861,SRR25519427,SRX21249690,SRS18503939,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO TFA 1  3dpf,GSM7681259,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO TFA 1  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681259,GSM7681259: zebrafish  DMSO TFA 1  3dpf; Danio rerio; RNA Seq,GSM7681259 r1,GSM7681259,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz,fastq fastq,8665981200.0,28886604.0,GSM7681259 r1,0:150 1:150,A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0,150,150,,,2086560929,2153111953,2157203992,2269104326,0,SRX21249690,SRS18503939,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71996,0.90816,0.03211,0.04297,0.77739,0.75097,0.5122,0.452,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24862,SRR25519428,SRX21249689,SRS18503938,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 4  3dpf,GSM7681258,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 4  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681258,GSM7681258: zebrafish  AR42 4  3dpf; Danio rerio; RNA Seq,GSM7681258 r1,GSM7681258,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_4.R1.fq.gz AR42_4.R2.fq.gz,fastq fastq,10199154900.0,33997183.0,GSM7681258 r1,0:150 1:150,A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0,150,150,,,2461755295,2524481077,2536143078,2676775450,0,SRX21249689,SRS18503938,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70676,0.89456,0.031,0.04108,0.77508,0.747,0.44642,0.47521,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24863,SRR25519429,SRX21249688,SRS18503937,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 3  3dpf,GSM7681257,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 3  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681257,GSM7681257: zebrafish  AR42 3  3dpf; Danio rerio; RNA Seq,GSM7681257 r1,GSM7681257,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_3.R1.fq.gz AR42_3.R2.fq.gz,fastq fastq,9953498100.0,33178327.0,GSM7681257 r1,0:150 1:150,A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0,150,150,,,2400858967,2463285586,2477369817,2611983730,0,SRX21249688,SRS18503937,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70865,0.89517,0.03101,0.04127,0.77325,0.74679,0.50253,0.50409,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24864,SRR25519430,SRX21249687,SRS18503936,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 2  3dpf,GSM7681256,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 2  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681256,GSM7681256: zebrafish  AR42 2  3dpf; Danio rerio; RNA Seq,GSM7681256 r1,GSM7681256,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_2.R1.fq.gz AR42_2.R2.fq.gz,fastq fastq,10005489000.0,33351630.0,GSM7681256 r1,0:150 1:150,A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0,150,150,,,2413672248,2477611702,2491304598,2622900452,0,SRX21249687,SRS18503936,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70639,0.89204,0.03035,0.04087,0.77502,0.74955,0.50558,0.50545,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24865,SRR25519431,SRX21249686,SRS18503935,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  AR42 1  3dpf,GSM7681255,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  AR42 1  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681255,GSM7681255: zebrafish  AR42 1  3dpf; Danio rerio; RNA Seq,GSM7681255 r1,GSM7681255,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_1.R1.fq.gz AR42_1.R2.fq.gz,fastq fastq,9698587800.0,32328626.0,GSM7681255 r1,0:150 1:150,A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0,150,150,,,2337968859,2400315331,2416067610,2544236000,0,SRX21249686,SRS18503935,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70903,0.89448,0.02976,0.04032,0.77583,0.74935,0.50747,0.5081,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24866,SRR25519432,SRX21249685,SRS18503934,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO 4  3dpf,GSM7681254,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO 4  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681254,GSM7681254: zebrafish  DMSO 4  3dpf; Danio rerio; RNA Seq,GSM7681254 r1,GSM7681254,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz,fastq fastq,9083670000.0,30278900.0,GSM7681254 r1,0:150 1:150,A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0,150,150,,,2191941100,2247936730,2258913579,2384878591,0,SRX21249685,SRS18503934,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71071,0.90457,0.03362,0.04688,0.77106,0.74357,0.50842,0.50975,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24867,SRR25519433,SRX21249684,SRS18503933,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO 3  3dpf,GSM7681253,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO 3  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681253,GSM7681253: zebrafish  DMSO 3  3dpf; Danio rerio; RNA Seq,GSM7681253 r1,GSM7681253,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz,fastq fastq,9394455000.0,31314850.0,GSM7681253 r1,0:150 1:150,A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0,150,150,,,2266296733,2324081714,2335347043,2468729510,0,SRX21249684,SRS18503933,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70975,0.90445,0.03329,0.04594,0.77005,0.7417,0.51188,0.5163,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24868,SRR25519434,SRX21249683,SRS18503932,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO 2  3dpf,GSM7681252,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO 2  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681252,GSM7681252: zebrafish  DMSO 2  3dpf; Danio rerio; RNA Seq,GSM7681252 r1,GSM7681252,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz,fastq fastq,9157453500.0,30524845.0,GSM7681252 r1,0:150 1:150,A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0,150,150,,,2209331568,2266614182,2273923578,2407584172,0,SRX21249683,SRS18503932,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70922,0.90538,0.03379,0.04616,0.7723,0.74213,0.50839,0.50803,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
24869,SRR25519435,SRX21249682,SRS18503931,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish  DMSO 1  3dpf,GSM7681251,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish  DMSO 1  3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co.  Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681251,GSM7681251: zebrafish  DMSO 1  3dpf; Danio rerio; RNA Seq,GSM7681251 r1,GSM7681251,1,RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz,fastq fastq,8769040200.0,29230134.0,GSM7681251 r1,0:150 1:150,A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0,150,150,,,2114427483,2170929931,2179906163,2303776623,0,SRX21249682,SRS18503931,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71002,0.9037,0.0335,0.04604,0.77155,0.74308,0.51339,0.50801,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system
25297,SRR25764099,SRX21486772,SRS18719072,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,Adult itgb4+ basal cells,GSM7734879,,tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,Adult itgb4+ basal cells,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734879,GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq,GSM7734879 r1,GSM7734879,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz,fastq fastq,5035430000.0,12588575.0,GSM7734879 r1,0:200 1:200,A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229,200,200,,,1339392170,1117195164,1254708952,1323174485,959229,SRX21486772,SRS18719072,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01543,0.02468,0.00098,0.00102,0.99318,0.99387,0.47878,0.31718,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Adult,Adult,Skin,Surface Structure
25298,SRR25764100,SRX21486771,SRS18719071,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep2,GSM7734878,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734878,GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq,GSM7734878 r1,GSM7734878,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz,fastq fastq,6040245600.0,15100614.0,GSM7734878 r1,0:200 1:200,A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625,200,200,,,1588346322,1356558310,1524614760,1569583583,1142625,SRX21486771,SRS18719071,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.0156,0.0191,0.00074,0.00093,0.99024,0.99088,0.47058,0.47838,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25299,SRR25764101,SRX21486770,SRS18719070,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep1,GSM7734877,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734877,GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq,GSM7734877 r1,GSM7734877,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz,fastq fastq,7055215600.0,17638039.0,GSM7734877 r1,0:200 1:200,A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146,200,200,,,1894635584,1556854856,1769420212,1825520802,8784146,SRX21486770,SRS18719070,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01135,0.01881,0.00043,0.00016,0.9932,0.99543,0.46234,0.43106,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25300,SRR25764102,SRX21486769,SRS18719069,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep2,GSM7734876,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734876,GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq,GSM7734876 r1,GSM7734876,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz,fastq fastq,9439207600.0,23598019.0,GSM7734876 r1,0:200 1:200,A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207,200,200,,,2499982675,2086665360,2395002073,2454282285,3275207,SRX21486769,SRS18719069,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.44931,0.01877,0.02236,0.00115,0.80012,0.99032,0.45473,0.49453,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25301,SRR25764103,SRX21486768,SRS18719066,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep1,GSM7734875,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734875,GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq,GSM7734875 r1,GSM7734875,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz,fastq fastq,6119547200.0,15298868.0,GSM7734875 r1,0:200 1:200,A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992,200,200,,,1642059769,1349462427,1535937964,1584527048,7559992,SRX21486768,SRS18719066,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01112,0.01017,0.0003,0.00014,0.9931,0.99586,0.43605,0.40821,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
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