metadata: run_metadata: 726 rows where experiment.library_source = "TRANSCRIPTOMIC" and tissue

726 rows where experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Tail"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	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.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
28818	28818	SRR26711836	SRX22410952	SRS19443730	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 4	GSM7885889	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885889	GSM7885889: rad21 heterozugous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885889 r1	GSM7885889	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-8-HET_S32_L001_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L001_R1_001.fastq.gz	fastq fastq	3261739218.0	21610373.0	GSM7885889 r1	0:75.52 1:75.42	A:816426262;C:810367718;G:804831968;T:829974289;N:138981	75	75			816426262	810367718	804831968	829974289	138981	SRX22410952	SRS19443730	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96738	0.97053	0.05473	0.05415	0.72283	0.72338	0.46691	0.46731	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28819	28819	SRR26711837	SRX22410952	SRS19443730	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 4	GSM7885889	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885889	GSM7885889: rad21 heterozugous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885889 r1	GSM7885889	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-8-HET_S32_L002_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L002_R1_001.fastq.gz	fastq fastq	3279254436.0	21726495.0	GSM7885889 r2	0:75.52 1:75.42	A:821154343;C:814711347;G:809025779;T:834224252;N:138715	75	75			821154343	814711347	809025779	834224252	138715	SRX22410952	SRS19443730	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96764	0.97012	0.05449	0.05364	0.72362	0.72478	0.46065	0.44816	75	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28820	28820	SRR26711838	SRX22410951	SRS19443729	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 4	GSM7885888	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885888	GSM7885888: rad21 homozygous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885888 r1	GSM7885888	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-4-MUT_S31_L001_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L001_R2_001.fastq.gz	fastq fastq	3815700579.0	25275353.0	GSM7885888 r1	0:75.53 1:75.43	A:962537652;C:941667596;G:934433379;T:976947974;N:113978	75	75			962537652	941667596	934433379	976947974	113978	SRX22410951	SRS19443729	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96535	0.96731	0.06446	0.06372	0.71928	0.71956	0.47233	0.47166	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28821	28821	SRR26711839	SRX22410951	SRS19443729	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 4	GSM7885888	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885888	GSM7885888: rad21 homozygous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885888 r1	GSM7885888	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-4-MUT_S31_L002_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L002_R2_001.fastq.gz	fastq fastq	3837906036.0	25422663.0	GSM7885888 r2	0:75.53 1:75.43	A:968455256;C:947191550;G:939808490;T:982330983;N:119757	75	75			968455256	947191550	939808490	982330983	119757	SRX22410951	SRS19443729	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96615	0.96781	0.0624	0.06196	0.71725	0.71827	0.47042	0.46294	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28822	28822	SRR26711840	SRX22410950	SRS19443727	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 4	GSM7885887	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885887	GSM7885887: rad21 heterozugous tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885887 r1	GSM7885887	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-8-HET_S30_L001_R2_001.fastq.gz Rad21-8-HET_S30_L001_R1_001.fastq.gz	fastq fastq	4150580457.0	27506773.0	GSM7885887 r1	0:75.51 1:75.39	A:1061191322;C:1016515755;G:1039117012;T:1033588629;N:167739	75	75			1061191322	1016515755	1039117012	1033588629	167739	SRX22410950	SRS19443727	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96699	0.96687	0.0501	0.04959	0.71642	0.72017	0.44914	0.44833	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28823	28823	SRR26711841	SRX22410950	SRS19443727	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 4	GSM7885887	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885887	GSM7885887: rad21 heterozugous tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885887 r1	GSM7885887	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-8-HET_S30_L002_R2_001.fastq.gz Rad21-8-HET_S30_L002_R1_001.fastq.gz	fastq fastq	4170430033.0	27638560.0	GSM7885887 r2	0:75.50 1:75.39	A:1067297262;C:1021226653;G:1043544460;T:1038184807;N:176851	75	75			1067297262	1021226653	1043544460	1038184807	176851	SRX22410950	SRS19443727	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96619	0.96635	0.05062	0.05015	0.7139	0.71918	0.44965	0.45175	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28824	28824	SRR26711842	SRX22410949	SRS19443728	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 4	GSM7885886	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885886	GSM7885886: rad21 homozygous tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885886 r1	GSM7885886	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-4-MUT_S29_L001_R1_001.fastq.gz Rad21-4-MUT_S29_L001_R2_001.fastq.gz	fastq fastq	3860758586.0	25585267.0	GSM7885886 r1	0:75.50 1:75.40	A:962978350;C:961963514;G:957530709;T:978120083;N:165930	75	75			962978350	961963514	957530709	978120083	165930	SRX22410949	SRS19443728	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96679	0.96899	0.05708	0.05592	0.71991	0.72021	0.44331	0.44736	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28825	28825	SRR26711843	SRX22410949	SRS19443728	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 4	GSM7885886	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885886	GSM7885886: rad21 homozygous tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885886 r1	GSM7885886	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-4-MUT_S29_L002_R1_001.fastq.gz Rad21-4-MUT_S29_L002_R2_001.fastq.gz	fastq fastq	3886411017.0	25755387.0	GSM7885886 r2	0:75.50 1:75.40	A:969709828;C:968345638;G:963787543;T:984390915;N:177093	75	75			969709828	968345638	963787543	984390915	177093	SRX22410949	SRS19443728	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96682	0.96836	0.05697	0.05624	0.71812	0.71819	0.4505	0.44685	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28826	28826	SRR26711844	SRX22410948	SRS19443726	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 4	GSM7885885	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885885	GSM7885885: stag2b tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885885 r1	GSM7885885	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-4_S28_L001_R1_001.fastq.gz S2B-BIO-4_S28_L001_R2_001.fastq.gz	fastq fastq	3727162917.0	24693169.0	GSM7885885 r1	0:75.53 1:75.41	A:922580573;C:935922329;G:933433047;T:935120514;N:106454	75	75			922580573	935922329	933433047	935120514	106454	SRX22410948	SRS19443726	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96731	0.96936	0.04393	0.04403	0.72234	0.72397	0.46015	0.45955	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28827	28827	SRR26711845	SRX22410948	SRS19443726	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 4	GSM7885885	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885885	GSM7885885: stag2b tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885885 r1	GSM7885885	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-4_S28_L002_R1_001.fastq.gz S2B-BIO-4_S28_L002_R2_001.fastq.gz	fastq fastq	3749916462.0	24844024.0	GSM7885885 r2	0:75.53 1:75.41	A:928588967;C:941571510;G:939049263;T:940598432;N:108290	75	75			928588967	941571510	939049263	940598432	108290	SRX22410948	SRS19443726	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96668	0.96881	0.04401	0.04387	0.72387	0.72519	0.45814	0.457	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28828	28828	SRR26711846	SRX22410947	SRS19443724	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 4	GSM7885884	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885884	GSM7885884: stag2b tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885884 r1	GSM7885884	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-4_S27_L001_R1_001.fastq.gz S2B-4_S27_L001_R2_001.fastq.gz	fastq fastq	4559287327.0	30217717.0	GSM7885884 r1	0:75.49 1:75.39	A:1129871064;C:1144626195;G:1141080047;T:1143531432;N:178589	75	75			1129871064	1144626195	1141080047	1143531432	178589	SRX22410947	SRS19443724	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96507	0.96728	0.04397	0.04385	0.72338	0.72456	0.44876	0.45623	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28829	28829	SRR26711847	SRX22410947	SRS19443724	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 4	GSM7885884	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885884	GSM7885884: stag2b tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885884 r1	GSM7885884	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-4_S27_L002_R1_001.fastq.gz S2B-4_S27_L002_R2_001.fastq.gz	fastq fastq	4586674313.0	30399355.0	GSM7885884 r2	0:75.49 1:75.39	A:1137101056;C:1151500029;G:1147768493;T:1150129054;N:175681	75	75			1137101056	1151500029	1147768493	1150129054	175681	SRX22410947	SRS19443724	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96454	0.96735	0.04449	0.04408	0.72435	0.72583	0.45339	0.45434	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28830	28830	SRR26711848	SRX22410946	SRS19443725	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 4	GSM7885883	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885883	GSM7885883: Wild type tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885883 r1	GSM7885883	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-4_S26_L001_R2_001.fastq.gz WT-BIO-4_S26_L001_R1_001.fastq.gz	fastq fastq	5251141754.0	34808166.0	GSM7885883 r1	0:75.48 1:75.38	A:1316653671;C:1303617399;G:1296205519;T:1334442750;N:222415	75	75			1316653671	1303617399	1296205519	1334442750	222415	SRX22410946	SRS19443725	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96497	0.96673	0.04868	0.04837	0.72332	0.72324	0.47006	0.45832	75	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28831	28831	SRR26711849	SRX22410946	SRS19443725	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 4	GSM7885883	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885883	GSM7885883: Wild type tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq	GSM7885883 r1	GSM7885883	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-4_S26_L002_R2_001.fastq.gz WT-BIO-4_S26_L002_R1_001.fastq.gz	fastq fastq	5280302307.0	35001391.0	GSM7885883 r2	0:75.48 1:75.38	A:1324401398;C:1310930748;G:1303177704;T:1341576726;N:215731	75	75			1324401398	1310930748	1303177704	1341576726	215731	SRX22410946	SRS19443725	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96424	0.96713	0.04917	0.04864	0.72241	0.72271	0.46443	0.45274	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28832	28832	SRR26711850	SRX22410945	SRS19443723	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 4	GSM7885882	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885882	GSM7885882: Wild type tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885882 r1	GSM7885882	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT4_S25_L001_R1_001.fastq.gz WT4_S25_L001_R2_001.fastq.gz	fastq fastq	7405469360.0	49089434.0	GSM7885882 r1	0:75.49 1:75.37	A:1847973647;C:1841169648;G:1840295933;T:1875743550;N:286582	75	75			1847973647	1841169648	1840295933	1875743550	286582	SRX22410945	SRS19443723	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96338	0.96738	0.04317	0.04296	0.71737	0.71851	0.45679	0.45543	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28833	28833	SRR26711851	SRX22410945	SRS19443723	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 4	GSM7885882	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 4	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885882	GSM7885882: Wild type tailbud no treatment replicate 4; Danio rerio; RNA Seq	GSM7885882 r1	GSM7885882	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT4_S25_L002_R1_001.fastq.gz WT4_S25_L002_R2_001.fastq.gz	fastq fastq	7449020435.0	49378676.0	GSM7885882 r2	0:75.48 1:75.37	A:1859225781;C:1852173354;G:1850890621;T:1886441454;N:289225	75	75			1859225781	1852173354	1850890621	1886441454	289225	SRX22410945	SRS19443723	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96307	0.9662	0.04334	0.04269	0.7167	0.71679	0.45909	0.45956	75	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28834	28834	SRR26711852	SRX22410944	SRS19443721	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 3	GSM7885881	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885881	GSM7885881: rad21 heterozugous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885881 r1	GSM7885881	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-7-HET_S24_L001_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L001_R2_001.fastq.gz	fastq fastq	3984218790.0	26397905.0	GSM7885881 r1	0:75.51 1:75.42	A:1024724878;C:960806363;G:958470013;T:1040115284;N:102252	75	75			1024724878	960806363	958470013	1040115284	102252	SRX22410944	SRS19443721	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95932	0.96163	0.06729	0.06702	0.71979	0.71981	0.4528	0.4607	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28835	28835	SRR26711853	SRX22410944	SRS19443721	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 3	GSM7885881	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885881	GSM7885881: rad21 heterozugous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885881 r1	GSM7885881	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-7-HET_S24_L002_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L002_R2_001.fastq.gz	fastq fastq	4008829445.0	26560912.0	GSM7885881 r2	0:75.51 1:75.42	A:1031275075;C:966838521;G:964312635;T:1046301501;N:101713	75	75			1031275075	966838521	964312635	1046301501	101713	SRX22410944	SRS19443721	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.9587	0.96152	0.06791	0.06665	0.71989	0.72157	0.45962	0.46712	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28836	28836	SRR26711854	SRX22410943	SRS19443722	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 3	GSM7885880	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885880	GSM7885880: rad21 homozygous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885880 r1	GSM7885880	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-3-MUT_S23_L001_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L001_R2_001.fastq.gz	fastq fastq	5599192259.0	37097144.0	GSM7885880 r1	0:75.51 1:75.43	A:1432393511;C:1358888032;G:1349825352;T:1457936919;N:148445	75	75			1432393511	1358888032	1349825352	1457936919	148445	SRX22410943	SRS19443722	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96008	0.96296	0.0752	0.07458	0.71518	0.71595	0.45869	0.45262	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28837	28837	SRR26711855	SRX22410943	SRS19443722	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 3	GSM7885880	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885880	GSM7885880: rad21 homozygous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885880 r1	GSM7885880	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-3-MUT_S23_L002_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L002_R2_001.fastq.gz	fastq fastq	5635998309.0	37340801.0	GSM7885880 r2	0:75.51 1:75.43	A:1442157325;C:1367898781;G:1358570964;T:1467225614;N:145625	75	75			1442157325	1367898781	1358570964	1467225614	145625	SRX22410943	SRS19443722	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95976	0.96205	0.07516	0.07494	0.71415	0.71498	0.4588	0.45974	75	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28838	28838	SRR26711856	SRX22410942	SRS19443720	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 3	GSM7885879	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885879	GSM7885879: rad21 heterozugous tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885879 r1	GSM7885879	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-7-HET_S22_L001_R1_001.fastq.gz Rad21-7-HET_S22_L001_R2_001.fastq.gz	fastq fastq	3991372523.0	26445612.0	GSM7885879 r1	0:75.50 1:75.43	A:1041422592;C:951170399;G:942539955;T:1056130915;N:108662	75	75			1041422592	951170399	942539955	1056130915	108662	SRX22410942	SRS19443720	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.956	0.9592	0.07986	0.07892	0.71336	0.71407	0.45912	0.45547	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28839	28839	SRR26711857	SRX22410942	SRS19443720	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 3	GSM7885879	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885879	GSM7885879: rad21 heterozugous tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885879 r1	GSM7885879	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-7-HET_S22_L002_R1_001.fastq.gz Rad21-7-HET_S22_L002_R2_001.fastq.gz	fastq fastq	4014736816.0	26600423.0	GSM7885879 r2	0:75.50 1:75.43	A:1047767788;C:956861322;G:947979944;T:1062023242;N:104520	75	75			1047767788	956861322	947979944	1062023242	104520	SRX22410942	SRS19443720	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95647	0.9597	0.07844	0.07753	0.71342	0.71449	0.45886	0.45627	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28840	28840	SRR26711858	SRX22410941	SRS19443719	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 3	GSM7885878	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885878	GSM7885878: rad21 homozygous tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885878 r1	GSM7885878	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-3-MUT_S21_L001_R1_001.fastq.gz Rad21-3-MUT_S21_L001_R2_001.fastq.gz	fastq fastq	4087719740.0	27096477.0	GSM7885878 r1	0:75.47 1:75.39	A:1036209125;C:1001425527;G:987804368;T:1062147338;N:133382	75	75			1036209125	1001425527	987804368	1062147338	133382	SRX22410941	SRS19443719	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95988	0.9638	0.06968	0.06927	0.71407	0.7136	0.454	0.45623	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28841	28841	SRR26711859	SRX22410941	SRS19443719	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 3	GSM7885878	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885878	GSM7885878: rad21 homozygous tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885878 r1	GSM7885878	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-3-MUT_S21_L002_R1_001.fastq.gz Rad21-3-MUT_S21_L002_R2_001.fastq.gz	fastq fastq	4118276880.0	27299338.0	GSM7885878 r2	0:75.47 1:75.38	A:1044090882;C:1009018215;G:995236418;T:1069786789;N:144576	75	75			1044090882	1009018215	995236418	1069786789	144576	SRX22410941	SRS19443719	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96038	0.96408	0.06924	0.06885	0.71405	0.71346	0.46106	0.46176	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28842	28842	SRR26711860	SRX22410940	SRS19443718	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 3	GSM7885877	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885877	GSM7885877: stag2b tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885877 r1	GSM7885877	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-3_S20_L001_R2_001.fastq.gz S2B-BIO-3_S20_L001_R1_001.fastq.gz	fastq fastq	6393544263.0	42359569.0	GSM7885877 r1	0:75.52 1:75.42	A:1613857834;C:1576676813;G:1555975373;T:1646885701;N:148542	75	75			1613857834	1576676813	1555975373	1646885701	148542	SRX22410940	SRS19443718	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96254	0.96412	0.05789	0.05657	0.71928	0.71952	0.45598	0.4571	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28843	28843	SRR26711861	SRX22410940	SRS19443718	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 3	GSM7885877	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885877	GSM7885877: stag2b tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885877 r1	GSM7885877	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-3_S20_L002_R1_001.fastq.gz S2B-BIO-3_S20_L002_R2_001.fastq.gz	fastq fastq	6434553541.0	42631351.0	GSM7885877 r2	0:75.52 1:75.42	A:1624553501;C:1586927728;G:1565855680;T:1657071521;N:145111	75	75			1624553501	1586927728	1565855680	1657071521	145111	SRX22410940	SRS19443718	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96161	0.96439	0.05708	0.057	0.71877	0.71885	0.45079	0.45162	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28844	28844	SRR26711862	SRX22410939	SRS19443717	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 3	GSM7885876	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885876	GSM7885876: stag2b tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885876 r1	GSM7885876	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-3_S19_L001_R2_001.fastq.gz S2B-3_S19_L001_R1_001.fastq.gz	fastq fastq	5538483383.0	36711860.0	GSM7885876 r1	0:75.47 1:75.39	A:1435032372;C:1328594066;G:1316913430;T:1457777034;N:166481	75	75			1435032372	1328594066	1316913430	1457777034	166481	SRX22410939	SRS19443717	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95388	0.95759	0.06115	0.05971	0.72494	0.72437	0.45251	0.45094	75	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28845	28845	SRR26711863	SRX22410939	SRS19443717	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 3	GSM7885876	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885876	GSM7885876: stag2b tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885876 r1	GSM7885876	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-3_S19_L002_R2_001.fastq.gz S2B-3_S19_L002_R1_001.fastq.gz	fastq fastq	5571956623.0	36933840.0	GSM7885876 r2	0:75.47 1:75.39	A:1444099757;C:1336600251;G:1324816524;T:1466267099;N:172992	75	75			1444099757	1336600251	1324816524	1466267099	172992	SRX22410939	SRS19443717	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95377	0.95715	0.06134	0.06056	0.72342	0.72399	0.45371	0.45229	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28846	28846	SRR26711864	SRX22410938	SRS19443716	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 3	GSM7885875	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885875	GSM7885875: Wild type tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885875 r1	GSM7885875	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-3_S18_L001_R2_001.fastq.gz WT-BIO-3_S18_L001_R1_001.fastq.gz	fastq fastq	2907588427.0	19272780.0	GSM7885875 r1	0:75.47 1:75.39	A:744742520;C:704673544;G:696135407;T:761933560;N:103396	75	75			744742520	704673544	696135407	761933560	103396	SRX22410938	SRS19443716	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95667	0.96068	0.06758	0.06662	0.71654	0.71695	0.46152	0.46391	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28847	28847	SRR26711865	SRX22410938	SRS19443716	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 3	GSM7885875	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885875	GSM7885875: Wild type tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq	GSM7885875 r1	GSM7885875	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-3_S18_L002_R2_001.fastq.gz WT-BIO-3_S18_L002_R1_001.fastq.gz	fastq fastq	2928304522.0	19409983.0	GSM7885875 r2	0:75.47 1:75.39	A:750212329;C:709699732;G:701107247;T:767185941;N:99273	75	75			750212329	709699732	701107247	767185941	99273	SRX22410938	SRS19443716	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95734	0.96043	0.06712	0.06582	0.71764	0.71829	0.46986	0.46257	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28848	28848	SRR26711866	SRX22410937	SRS19443715	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 3	GSM7885874	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885874	GSM7885874: Wild type tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885874 r1	GSM7885874	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT3_S17_L001_R2_001.fastq.gz WT3_S17_L001_R1_001.fastq.gz	fastq fastq	6706792771.0	44471190.0	GSM7885874 r1	0:75.45 1:75.37	A:1721256764;C:1618398945;G:1602221748;T:1764649478;N:265836	75	75			1721256764	1618398945	1602221748	1764649478	265836	SRX22410937	SRS19443715	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95476	0.95901	0.0654	0.06441	0.71821	0.71764	0.46826	0.46883	75	73	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28849	28849	SRR26711867	SRX22410937	SRS19443715	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 3	GSM7885874	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 3	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885874	GSM7885874: Wild type tailbud no treatment replicate 3; Danio rerio; RNA Seq	GSM7885874 r1	GSM7885874	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT3_S17_L002_R1_001.fastq.gz WT3_S17_L002_R2_001.fastq.gz	fastq fastq	6751557772.0	44768192.0	GSM7885874 r2	0:75.45 1:75.37	A:1732864650;C:1629248349;G:1613082990;T:1776088109;N:273674	75	75			1732864650	1629248349	1613082990	1776088109	273674	SRX22410937	SRS19443715	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95584	0.95991	0.0649	0.0638	0.71819	0.71855	0.47015	0.46826	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28850	28850	SRR26711868	SRX22410936	SRS19443714	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 2	GSM7885873	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885873	GSM7885873: rad21 heterozugous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885873 r1	GSM7885873	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-6-HET_S16_L001_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L001_R2_001.fastq.gz	fastq fastq	10402910048.0	68936909.0	GSM7885873 r1	0:75.49 1:75.41	A:2678222257;C:2507951720;G:2508878864;T:2707580436;N:276771	75	75			2678222257	2507951720	2508878864	2707580436	276771	SRX22410936	SRS19443714	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95996	0.96303	0.07074	0.07121	0.7176	0.71977	0.46271	0.46279	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28851	28851	SRR26711869	SRX22410936	SRS19443714	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 2	GSM7885873	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885873	GSM7885873: rad21 heterozugous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885873 r1	GSM7885873	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-6-HET_S16_L002_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L002_R2_001.fastq.gz	fastq fastq	10457419135.0	69298126.0	GSM7885873 r2	0:75.49 1:75.41	A:2693018275;C:2521215208;G:2521858256;T:2721040335;N:287061	75	75			2693018275	2521215208	2521858256	2721040335	287061	SRX22410936	SRS19443714	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95978	0.962	0.07287	0.07218	0.71928	0.72015	0.4627	0.46327	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28852	28852	SRR26711870	SRX22410935	SRS19443713	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 2	GSM7885872	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885872	GSM7885872: rad21 homozygous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885872 r1	GSM7885872	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-2-MUT_S15_L001_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L001_R1_001.fastq.gz	fastq fastq	7186685076.0	47626097.0	GSM7885872 r1	0:75.50 1:75.40	A:1840710532;C:1745543326;G:1746892421;T:1853340863;N:197934	75	75			1840710532	1745543326	1746892421	1853340863	197934	SRX22410935	SRS19443713	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96231	0.96418	0.06946	0.06881	0.71756	0.71873	0.46166	0.45998	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28853	28853	SRR26711871	SRX22410935	SRS19443713	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 2	GSM7885872	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885872	GSM7885872: rad21 homozygous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885872 r1	GSM7885872	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-2-MUT_S15_L002_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L002_R1_001.fastq.gz	fastq fastq	7224888168.0	47879502.0	GSM7885872 r2	0:75.50 1:75.40	A:1851188490;C:1754962659;G:1755894085;T:1862643357;N:199577	75	75			1851188490	1754962659	1755894085	1862643357	199577	SRX22410935	SRS19443713	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96174	0.96335	0.06858	0.06794	0.71624	0.71752	0.46477	0.46238	74	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28854	28854	SRR26711872	SRX22410934	SRS19443712	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 2	GSM7885871	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885871	GSM7885871: rad21 heterozugous tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885871 r1	GSM7885871	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-6-HET_S14_L001_R2_001.fastq.gz Rad21-6-HET_S14_L001_R1_001.fastq.gz	fastq fastq	5920802946.0	39225537.0	GSM7885871 r1	0:75.52 1:75.42	A:1518148809;C:1443498311;G:1449929695;T:1509064332;N:161799	75	75			1518148809	1443498311	1449929695	1509064332	161799	SRX22410934	SRS19443712	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96404	0.96544	0.06392	0.06339	0.71825	0.71956	0.45911	0.44993	75	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28855	28855	SRR26711873	SRX22410934	SRS19443712	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 2	GSM7885871	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885871	GSM7885871: rad21 heterozugous tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885871 r1	GSM7885871	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-6-HET_S14_L002_R1_001.fastq.gz Rad21-6-HET_S14_L002_R2_001.fastq.gz	fastq fastq	5948197274.0	39406919.0	GSM7885871 r2	0:75.52 1:75.42	A:1525770407;C:1450296537;G:1456334492;T:1515638367;N:157471	75	75			1525770407	1450296537	1456334492	1515638367	157471	SRX22410934	SRS19443712	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.9635	0.96517	0.06272	0.06248	0.71804	0.72202	0.45512	0.45879	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28856	28856	SRR26711874	SRX22410933	SRS19443711	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 2	GSM7885870	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885870	GSM7885870: rad21 homozygous tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885870 r1	GSM7885870	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-9-MUT_S13_L001_R2_001.fastq.gz Rad21-9-MUT_S13_L001_R1_001.fastq.gz	fastq fastq	4731957733.0	31354997.0	GSM7885870 r1	0:75.51 1:75.41	A:1201221275;C:1160116117;G:1163056871;T:1207419408;N:144062	75	75			1201221275	1160116117	1163056871	1207419408	144062	SRX22410933	SRS19443711	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96425	0.96472	0.06588	0.06468	0.71687	0.71942	0.4434	0.44236	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28857	28857	SRR26711875	SRX22410933	SRS19443711	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 2	GSM7885870	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885870	GSM7885870: rad21 homozygous tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885870 r1	GSM7885870	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-9-MUT_S13_L002_R1_001.fastq.gz Rad21-9-MUT_S13_L002_R2_001.fastq.gz	fastq fastq	4757933550.0	31527251.0	GSM7885870 r2	0:75.51 1:75.41	A:1208392417;C:1166483269;G:1169184243;T:1213729419;N:144202	75	75			1208392417	1166483269	1169184243	1213729419	144202	SRX22410933	SRS19443711	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96375	0.96493	0.06559	0.06422	0.71774	0.71922	0.44693	0.43358	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28858	28858	SRR26711876	SRX22410932	SRS19443710	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 2	GSM7885869	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885869	GSM7885869: stag2b tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885869 r1	GSM7885869	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-2_S12_L001_R1_001.fastq.gz S2B-BIO-2_S12_L001_R2_001.fastq.gz	fastq fastq	3434334163.0	22753985.0	GSM7885869 r1	0:75.51 1:75.42	A:874466456;C:839309146;G:839975055;T:880508590;N:74916	75	75			874466456	839309146	839975055	880508590	74916	SRX22410932	SRS19443710	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96096	0.96302	0.06063	0.06064	0.71676	0.7177	0.45781	0.45685	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28859	28859	SRR26711877	SRX22410932	SRS19443710	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 2	GSM7885869	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885869	GSM7885869: stag2b tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885869 r1	GSM7885869	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-2_S12_L002_R1_001.fastq.gz S2B-BIO-2_S12_L002_R2_001.fastq.gz	fastq fastq	3455106879.0	22891438.0	GSM7885869 r2	0:75.52 1:75.42	A:880118959;C:844367467;G:844856793;T:885694827;N:68833	75	75			880118959	844367467	844856793	885694827	68833	SRX22410932	SRS19443710	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96044	0.96247	0.06148	0.06124	0.71892	0.72019	0.45384	0.45979	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28860	28860	SRR26711878	SRX22410931	SRS19443708	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 2	GSM7885868	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885868	GSM7885868: stag2b tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885868 r1	GSM7885868	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-2_S11_L001_R1_001.fastq.gz S2B-2_S11_L001_R2_001.fastq.gz	fastq fastq	3538294337.0	23437308.0	GSM7885868 r1	0:75.53 1:75.44	A:911440182;C:854797688;G:851200714;T:920789817;N:65936	75	75			911440182	854797688	851200714	920789817	65936	SRX22410931	SRS19443708	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95621	0.95881	0.06034	0.05969	0.71816	0.71892	0.45142	0.45093	75	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28861	28861	SRR26711879	SRX22410931	SRS19443708	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 2	GSM7885868	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885868	GSM7885868: stag2b tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885868 r1	GSM7885868	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-2_S11_L002_R1_001.fastq.gz S2B-2_S11_L002_R2_001.fastq.gz	fastq fastq	3556484158.0	23557941.0	GSM7885868 r2	0:75.53 1:75.44	A:916293958;C:859339499;G:855534732;T:925247442;N:68527	75	75			916293958	859339499	855534732	925247442	68527	SRX22410931	SRS19443708	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95449	0.95714	0.05993	0.05895	0.7207	0.72174	0.44213	0.44014	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28862	28862	SRR26711880	SRX22410930	SRS19443709	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 2	GSM7885867	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885867	GSM7885867: Wild type tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885867 r1	GSM7885867	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-2_S10_L001_R1_001.fastq.gz WT-BIO-2_S10_L001_R2_001.fastq.gz	fastq fastq	4962467069.0	32885292.0	GSM7885867 r1	0:75.49 1:75.41	A:1261895016;C:1212881283;G:1199367390;T:1288195310;N:128070	75	75			1261895016	1212881283	1199367390	1288195310	128070	SRX22410930	SRS19443709	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96086	0.96361	0.06058	0.05969	0.71679	0.71614	0.46741	0.47167	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28863	28863	SRR26711881	SRX22410930	SRS19443709	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 2	GSM7885867	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885867	GSM7885867: Wild type tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq	GSM7885867 r1	GSM7885867	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-2_S10_L002_R1_001.fastq.gz WT-BIO-2_S10_L002_R2_001.fastq.gz	fastq fastq	4987807658.0	33053054.0	GSM7885867 r2	0:75.50 1:75.41	A:1268585681;C:1219140011;G:1205507373;T:1294443086;N:131507	75	75			1268585681	1219140011	1205507373	1294443086	131507	SRX22410930	SRS19443709	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96019	0.96278	0.0598	0.05932	0.71837	0.71942	0.46581	0.46052	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28864	28864	SRR26711882	SRX22410929	SRS19443707	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 2	GSM7885866	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885866	GSM7885866: Wild type tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885866 r1	GSM7885866	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT2_S9_L001_R1_001.fastq.gz WT2_S9_L001_R2_001.fastq.gz	fastq fastq	4886840867.0	32385548.0	GSM7885866 r1	0:75.49 1:75.41	A:1236862700;C:1194914216;G:1187547323;T:1267379660;N:136968	75	75			1236862700	1194914216	1187547323	1267379660	136968	SRX22410929	SRS19443707	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95919	0.96199	0.05896	0.0586	0.71555	0.71587	0.46036	0.46125	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28865	28865	SRR26711883	SRX22410929	SRS19443707	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 2	GSM7885866	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 2	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885866	GSM7885866: Wild type tailbud no treatment replicate 2; Danio rerio; RNA Seq	GSM7885866 r1	GSM7885866	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT2_S9_L002_R1_001.fastq.gz WT2_S9_L002_R2_001.fastq.gz	fastq fastq	4916008107.0	32579134.0	GSM7885866 r2	0:75.49 1:75.40	A:1244399521;C:1202192346;G:1194561433;T:1274714960;N:139847	75	75			1244399521	1202192346	1194561433	1274714960	139847	SRX22410929	SRS19443707	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.95906	0.9626	0.05798	0.05754	0.71502	0.71526	0.46094	0.45988	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28866	28866	SRR26711884	SRX22410928	SRS19443706	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 1	GSM7885865	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885865	GSM7885865: rad21 heterozugous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885865 r1	GSM7885865	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-5-HET_S8_L001_R1_001.fastq.gz Rad21-BIO-5-HET_S8_L001_R2_001.fastq.gz	fastq fastq	3066593621.0	20312935.0	GSM7885865 r1	0:75.54 1:75.43	A:773539057;C:758309818;G:762855989;T:771829322;N:59435	75	75			773539057	758309818	762855989	771829322	59435	SRX22410928	SRS19443706	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.93814	0.93898	0.05206	0.05092	0.72403	0.72606	0.45323	0.45594	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28867	28867	SRR26711885	SRX22410928	SRS19443706	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud Wnt stimulation replicate 1	GSM7885865	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885865	GSM7885865: rad21 heterozugous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885865 r1	GSM7885865	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-5-HET_S8_L002_R1_001.fastq.gz Rad21-BIO-5-HET_S8_L002_R2_001.fastq.gz	fastq fastq	3080824265.0	20407318.0	GSM7885865 r2	0:75.54 1:75.43	A:777565943;C:761729558;G:766237246;T:775229684;N:61834	75	75			777565943	761729558	766237246	775229684	61834	SRX22410928	SRS19443706	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.93811	0.93851	0.0524	0.05135	0.72403	0.72689	0.45207	0.46155	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28868	28868	SRR26711886	SRX22410927	SRS19443704	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 1	GSM7885864	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885864	GSM7885864: rad21 homozygous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885864 r1	GSM7885864	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-1-MUT_S7_L001_R1_001.fastq.gz Rad21-BIO-1-MUT_S7_L001_R2_001.fastq.gz	fastq fastq	4788638898.0	31734845.0	GSM7885864 r1	0:75.51 1:75.38	A:1180996230;C:1208056992;G:1207225278;T:1192209164;N:151234	75	75			1180996230	1208056992	1207225278	1192209164	151234	SRX22410927	SRS19443704	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.971	0.97197	0.04922	0.04884	0.72342	0.72571	0.46723	0.46582	75	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28869	28869	SRR26711887	SRX22410927	SRS19443704	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud Wnt stimulation replicate 1	GSM7885864	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant\|treatment:Wnt signaling stimulation	GSM7885864	GSM7885864: rad21 homozygous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885864 r1	GSM7885864	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-BIO-1-MUT_S7_L002_R1_001.fastq.gz Rad21-BIO-1-MUT_S7_L002_R2_001.fastq.gz	fastq fastq	4815323290.0	31911994.0	GSM7885864 r2	0:75.51 1:75.38	A:1187948393;C:1214824723;G:1213764297;T:1198630801;N:155076	75	75			1187948393	1214824723	1213764297	1198630801	155076	SRX22410927	SRS19443704	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.97042	0.97163	0.04919	0.04822	0.72575	0.72725	0.46784	0.46687	75	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28870	28870	SRR26711888	SRX22410926	SRS19443705	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 1	GSM7885863	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885863	GSM7885863: rad21 heterozugous tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885863 r1	GSM7885863	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-5-HET_S6_L001_R1_001.fastq.gz Rad21-5-HET_S6_L001_R2_001.fastq.gz	fastq fastq	4731947877.0	31344805.0	GSM7885863 r1	0:75.54 1:75.42	A:1174667885;C:1187877616;G:1186233757;T:1183073645;N:94974	75	75			1174667885	1187877616	1186233757	1183073645	94974	SRX22410926	SRS19443705	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.97019	0.97104	0.04787	0.04709	0.72013	0.72157	0.45904	0.4534	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28871	28871	SRR26711889	SRX22410926	SRS19443705	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 heterozugous tailbud no treatment replicate 1	GSM7885863	source name:tailbud\|tissue:tailbud\|genotype:heterozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 heterozugous tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:heterozygous rad21 mutant	GSM7885863	GSM7885863: rad21 heterozugous tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885863 r1	GSM7885863	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-5-HET_S6_L002_R2_001.fastq.gz Rad21-5-HET_S6_L002_R1_001.fastq.gz	fastq fastq	4753935677.0	31490466.0	GSM7885863 r2	0:75.54 1:75.42	A:1180603224;C:1193421384;G:1191530186;T:1188281161;N:99722	75	75			1180603224	1193421384	1191530186	1188281161	99722	SRX22410926	SRS19443705	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96921	0.97138	0.04824	0.04771	0.72135	0.72253	0.4575	0.45266	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28872	28872	SRR26711890	SRX22410925	SRS19443703	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 1	GSM7885862	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885862	GSM7885862: rad21 homozygous tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885862 r1	GSM7885862	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-1-MUT_S5_L001_R1_001.fastq.gz Rad21-1-MUT_S5_L001_R2_001.fastq.gz	fastq fastq	4118085890.0	27306618.0	GSM7885862 r1	0:75.47 1:75.34	A:1025300027;C:1029335773;G:1030828275;T:1032469485;N:152330	75	75			1025300027	1029335773	1030828275	1032469485	152330	SRX22410925	SRS19443703	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96791	0.96862	0.05188	0.0515	0.72013	0.72015	0.4522	0.4471	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28873	28873	SRR26711891	SRX22410925	SRS19443703	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	rad21 homozygous tailbud no treatment replicate 1	GSM7885862	source name:tailbud\|tissue:tailbud\|genotype:homozygous rad21 mutant\|geo loc name:missing\|collection date:missing	rad21 homozygous tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous rad21 mutant	GSM7885862	GSM7885862: rad21 homozygous tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885862 r1	GSM7885862	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	Rad21-1-MUT_S5_L002_R1_001.fastq.gz Rad21-1-MUT_S5_L002_R2_001.fastq.gz	fastq fastq	4146986760.0	27498264.0	GSM7885862 r2	0:75.47 1:75.34	A:1032908199;C:1036610487;G:1037792727;T:1039516300;N:159047	75	75			1032908199	1036610487	1037792727	1039516300	159047	SRX22410925	SRS19443703	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96742	0.96892	0.05165	0.05113	0.71918	0.72068	0.45142	0.45319	76	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28874	28874	SRR26711892	SRX22410924	SRS19443702	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 1	GSM7885861	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885861	GSM7885861: stag2b tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885861 r1	GSM7885861	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-1_S4_L001_R2_001.fastq.gz S2B-BIO-1_S4_L001_R1_001.fastq.gz	fastq fastq	2897013924.0	19254896.0	GSM7885861 r1	0:75.29 1:75.17	A:741141530;C:706870086;G:710814654;T:738037384;N:150270	75	75			741141530	706870086	710814654	738037384	150270	SRX22410924	SRS19443702	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96485	0.96632	0.05089	0.05075	0.72423	0.72638	0.46419	0.4639	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28875	28875	SRR26711893	SRX22410924	SRS19443702	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud Wnt stimulation replicate 1	GSM7885861	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	stag2b tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant\|treatment:Wnt signaling stimulation	GSM7885861	GSM7885861: stag2b tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885861 r1	GSM7885861	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-BIO-1_S4_L002_R1_001.fastq.gz S2B-BIO-1_S4_L002_R2_001.fastq.gz	fastq fastq	2915617733.0	19378751.0	GSM7885861 r2	0:75.29 1:75.17	A:746370200;C:711440488;G:715102603;T:742552430;N:152012	75	75			746370200	711440488	715102603	742552430	152012	SRX22410924	SRS19443702	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96529	0.96741	0.05064	0.05044	0.72397	0.7259	0.47066	0.47479	75	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28876	28876	SRR26711894	SRX22410923	SRS19443701	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 1	GSM7885860	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885860	GSM7885860: stag2b tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885860 r1	GSM7885860	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-1_S3_L001_R1_001.fastq.gz S2B-1_S3_L001_R2_001.fastq.gz	fastq fastq	4816347042.0	31912880.0	GSM7885860 r1	0:75.52 1:75.40	A:1186516295;C:1215887273;G:1212449212;T:1201357694;N:136568	75	75			1186516295	1215887273	1212449212	1201357694	136568	SRX22410923	SRS19443701	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96723	0.96949	0.03922	0.039	0.72417	0.72563	0.44797	0.44612	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28877	28877	SRR26711895	SRX22410923	SRS19443701	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	stag2b tailbud no treatment replicate 1	GSM7885860	source name:tailbud\|tissue:tailbud\|genotype:homozygous stag2b mutant\|geo loc name:missing\|collection date:missing	stag2b tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:homozygous stag2b mutant	GSM7885860	GSM7885860: stag2b tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885860 r1	GSM7885860	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	S2B-1_S3_L002_R1_001.fastq.gz S2B-1_S3_L002_R2_001.fastq.gz	fastq fastq	4844499098.0	32099402.0	GSM7885860 r2	0:75.52 1:75.40	A:1193956975;C:1222998516;G:1219273844;T:1208134191;N:135572	75	75			1193956975	1222998516	1219273844	1208134191	135572	SRX22410923	SRS19443701	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.9673	0.96927	0.03901	0.03847	0.72265	0.7237	0.44466	0.44733	75	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28878	28878	SRR26711896	SRX22410922	SRS19443700	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 1	GSM7885859	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885859	GSM7885859: Wild type tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885859 r1	GSM7885859	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-1_S2_L001_R1_001.fastq.gz WT-BIO-1_S2_L001_R2_001.fastq.gz	fastq fastq	5412178875.0	35866424.0	GSM7885859 r1	0:75.51 1:75.39	A:1366497169;C:1337079143;G:1340668569;T:1367824895;N:109099	75	75			1366497169	1337079143	1340668569	1367824895	109099	SRX22410922	SRS19443700	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96469	0.96636	0.05031	0.04926	0.71792	0.71985	0.46735	0.46003	76	76	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28879	28879	SRR26711897	SRX22410922	SRS19443700	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud Wnt stimulation replicate 1	GSM7885859	source name:tailbud\|tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation\|geo loc name:missing\|collection date:missing	Wild type tailbud Wnt stimulation replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type\|treatment:Wnt signaling stimulation	GSM7885859	GSM7885859: Wild type tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq	GSM7885859 r1	GSM7885859	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT-BIO-1_S2_L002_R1_001.fastq.gz WT-BIO-1_S2_L002_R2_001.fastq.gz	fastq fastq	5439582943.0	36048596.0	GSM7885859 r2	0:75.50 1:75.39	A:1374188816;C:1343757292;G:1347041961;T:1374478321;N:116553	75	75			1374188816	1343757292	1347041961	1374478321	116553	SRX22410922	SRS19443700	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96388	0.96569	0.04966	0.04871	0.71959	0.72141	0.46438	0.47241	76	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28880	28880	SRR26711898	SRX22410921	SRS19443699	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 1	GSM7885858	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885858	GSM7885858: Wild type tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885858 r1	GSM7885858	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT1_S1_L001_R2_001.fastq.gz WT1_S1_L001_R1_001.fastq.gz	fastq fastq	4648127675.0	30828112.0	GSM7885858 r1	0:75.45 1:75.32	A:1143762350;C:1169301499;G:1170916895;T:1163919823;N:227108	75	75			1143762350	1169301499	1170916895	1163919823	227108	SRX22410921	SRS19443699	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96756	0.96895	0.03865	0.03806	0.73275	0.73521	0.4512	0.44878	74	74	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
28881	28881	SRR26711899	SRX22410921	SRS19443699	SRP470622	PRJNA1036688	Cohesin composition and dosage independently affect early development in zebrafish	GSE247246	Transcriptome Analysis	Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.	pubmed:38975838	Wild type tailbud no treatment replicate 1	GSM7885858	source name:tailbud\|tissue:tailbud\|genotype:wild type\|geo loc name:missing\|collection date:missing	Wild type tailbud no treatment replicate 1	Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups	tailbud	2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	E3 media 28 C	tissue:tailbud\|genotype:wild type	GSM7885858	GSM7885858: Wild type tailbud no treatment replicate 1; Danio rerio; RNA Seq	GSM7885858 r1	GSM7885858	1	RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP470622	loader:fastq load.py	WT1_S1_L002_R1_001.fastq.gz WT1_S1_L002_R2_001.fastq.gz	fastq fastq	4676143483.0	31014103.0	GSM7885858 r2	0:75.45 1:75.32	A:1151068941;C:1176347620;G:1177720113;T:1170778976;N:227833	75	75			1151068941	1176347620	1177720113	1170778976	227833	SRX22410921	SRS19443699	SRA1747076	Chromosome Structure and Development, Pathology, Otago University	Chromosome Structure and Development, Pathology, Otago University	2	0.96645	0.96872	0.03855	0.03822	0.73486	0.73513	0.4505	0.4476	73	75	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	New Zealand	2023-11-07	Multi-stage	Embryo	Tail	Multi-system
32781	32781	SRR29411985	SRX24925451	SRS21630866	SRP513930	PRJNA1124008	Cell state transitions are decoupled from cell division during early embryo development [II]	GSE269848	Other	Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…	pubmed:37546736	24 38 hpf and 48 hpf tails	GSM8328864	source name:embryo tail\|tissue:embryo tail\|geo loc name:missing\|collection date:missing	24 38 hpf and 48 hpf tails	Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f…	embryo tail		Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		tissue:embryo tail	GSM8328864	GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER	GSM8328864 r1	GSM8328864	1	Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP513930		Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz	fastq fastq fastq fastq	58603546956.0	505202991.0	GSM8328864 r1	0:86 1:8 2:8 3:14	A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340	86	8	8	14	13191204330	9162028793	9431065581	11662090182	1068340	SRX24925451	SRS21630866	SRA1899240	Harvard University	Harvard University												B		usable mapping rate	illumina	novaseq_era	unknown	other	trueseq	sc	single_cell_droplet	indrops	United States	2024-06-14	Multi-stage	Embryo	Tail	Multi-system
32782	32782	SRR29411986	SRX24925451	SRS21630866	SRP513930	PRJNA1124008	Cell state transitions are decoupled from cell division during early embryo development [II]	GSE269848	Other	Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…	pubmed:37546736	24 38 hpf and 48 hpf tails	GSM8328864	source name:embryo tail\|tissue:embryo tail\|geo loc name:missing\|collection date:missing	24 38 hpf and 48 hpf tails	Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f…	embryo tail		Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		tissue:embryo tail	GSM8328864	GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER	GSM8328864 r1	GSM8328864	1	Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP513930		Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz	fastq fastq fastq fastq	44072422880.0	379934680.0	GSM8328864 r2	0:86 1:8 2:8 3:14	A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152	86	8	8	14	9919784228	6894965731	7094749745	8764100624	782152	SRX24925451	SRS21630866	SRA1899240	Harvard University	Harvard University												B		usable mapping rate	illumina	novaseq_era	unknown	other	trueseq	sc	single_cell_droplet	indrops	United States	2024-06-14	Multi-stage	Embryo	Tail	Multi-system
36147	36147	SRR33446914	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-4_S18_L001_R1_001.fastq.gz	fastq	392062720.0	5158720.0	GSM8970925 r1	0:76	A:111393933;C:84178440;G:86759120;T:109728583;N:2644	76				111393933	84178440	86759120	109728583	2644	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36148	36148	SRR33446915	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-4_S18_L002_R1_001.fastq.gz	fastq	382539160.0	5033410.0	GSM8970925 r2	0:76	A:108549273;C:82135694;G:84877971;T:106974218;N:2004	76				108549273	82135694	84877971	106974218	2004	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36149	36149	SRR33446916	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-4_S18_L003_R1_001.fastq.gz	fastq	390689020.0	5140645.0	GSM8970925 r3	0:76	A:110921885;C:83926202;G:86538209;T:109300187;N:2537	76				110921885	83926202	86538209	109300187	2537	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36150	36150	SRR33446917	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-4_S18_L004_R1_001.fastq.gz	fastq	385026032.0	5066132.0	GSM8970925 r4	0:76	A:109282089;C:82666299;G:85291625;T:107783812;N:2207	76				109282089	82666299	85291625	107783812	2207	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36151	36151	SRR33446918	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-3_S17_L001_R1_001.fastq.gz	fastq	242078544.0	3185244.0	GSM8970924 r1	0:76	A:70805011;C:50935537;G:52720022;T:67616569;N:1405	76				70805011	50935537	52720022	67616569	1405	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36152	36152	SRR33446919	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-3_S17_L002_R1_001.fastq.gz	fastq	236879840.0	3116840.0	GSM8970924 r2	0:76	A:69118193;C:49900432;G:51722708;T:66137243;N:1264	76				69118193	49900432	51722708	66137243	1264	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36153	36153	SRR33446920	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-3_S17_L003_R1_001.fastq.gz	fastq	241246952.0	3174302.0	GSM8970924 r3	0:76	A:70493049;C:50814403;G:52594412;T:67343618;N:1470	76				70493049	50814403	52594412	67343618	1470	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36154	36154	SRR33446921	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-3_S17_L004_R1_001.fastq.gz	fastq	238296936.0	3135486.0	GSM8970924 r4	0:76	A:69600911;C:50177666;G:51934697;T:66582348;N:1314	76				69600911	50177666	51934697	66582348	1314	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36155	36155	SRR33446922	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-2_S16_L001_R1_001.fastq.gz	fastq	293546884.0	3862459.0	GSM8970923 r1	0:76	A:86721485;C:61000183;G:63592308;T:82231012;N:1896	76				86721485	61000183	63592308	82231012	1896	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36156	36156	SRR33446923	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-2_S16_L002_R1_001.fastq.gz	fastq	287313668.0	3780443.0	GSM8970923 r2	0:76	A:84719789;C:59732524;G:62422596;T:80437282;N:1477	76				84719789	59732524	62422596	80437282	1477	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36157	36157	SRR33446924	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-2_S16_L003_R1_001.fastq.gz	fastq	293081612.0	3856337.0	GSM8970923 r3	0:76	A:86491724;C:60944765;G:63551581;T:82091805;N:1737	76				86491724	60944765	63551581	82091805	1737	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36158	36158	SRR33446925	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		White-2_S16_L004_R1_001.fastq.gz	fastq	289340284.0	3807109.0	GSM8970923 r4	0:76	A:85390241;C:60135471;G:62741618;T:81071340;N:1614	76				85390241	60135471	62741618	81071340	1614	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36159	36159	SRR33446926	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		Red-4_S15_L001_R1_001.fastq.gz	fastq	293676616.0	3864166.0	GSM8970922 r1	0:76	A:85055525;C:61514402;G:62951777;T:84153135;N:1777	76				85055525	61514402	62951777	84153135	1777	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36160	36160	SRR33446927	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		Red-4_S15_L002_R1_001.fastq.gz	fastq	287550712.0	3783562.0	GSM8970922 r2	0:76	A:83130155;C:60249305;G:61817163;T:82352632;N:1457	76				83130155	60249305	61817163	82352632	1457	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36161	36161	SRR33446928	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		Red-4_S15_L003_R1_001.fastq.gz	fastq	293005460.0	3855335.0	GSM8970922 r3	0:76	A:84798214;C:61435286;G:62865004;T:83905146;N:1810	76				84798214	61435286	62865004	83905146	1810	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36162	36162	SRR33446929	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		Red-4_S15_L004_R1_001.fastq.gz	fastq	289004668.0	3802693.0	GSM8970922 r4	0:76	A:83595831;C:60570265;G:62006632;T:82830364;N:1576	76				83595831	60570265	62006632	82830364	1576	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36163	36163	SRR33446930	SRX28687229	SRS24954085	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 3	GSM8970921	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970921	GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970921 r1	GSM8970921	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		Red-3_S14_L001_R1_001.fastq.gz	fastq	300231768.0	3950418.0	GSM8970921 r1	0:76	A:88106516;C:61818857;G:65466450;T:84838096;N:1849	76				88106516	61818857	65466450	84838096	1849	SRX28687229	SRS24954085	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36164	36164	SRR33446931	SRX28687229	SRS24954085	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 3	GSM8970921	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970921	GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970921 r1	GSM8970921	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP583344		Red-3_S14_L002_R1_001.fastq.gz	fastq	293677452.0	3864177.0	GSM8970921 r2	0:76	A:86015379;C:60508410;G:64229226;T:82922956;N:1481	76				86015379	60508410	64229226	82922956	1481	SRX28687229	SRS24954085	SRA2124571	University of Sheffield	University of Sheffield												B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-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");;