metadata: run_metadata: 1,425 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "cDNA" and experiment.platform = "DNBSEQ"

1,425 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "cDNA" and experiment.platform = "DNBSEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
44	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;