metadata: run_metadata: 1,308 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" and technology = "generic-scrnaseq-only"

1,308 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" and technology = "generic-scrnaseq-only"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.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
28611	28611	SRR26471890	SRX22175831	SRS19233331	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb mut eos 2	GSM7854238	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb mut eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP	GSM7854238	GSM7854238: cebpb mut eos 2; Danio rerio; RNA Seq	GSM7854238 r1	GSM7854238	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	F2_1.fq.gz F2_2.fq.gz	fastq fastq	6304806000.0	21016020.0	GSM7854238 r1	0:150 1:150	A:1797551316;C:1332146220;G:1348919312;T:1826125402;N:63750	150	150	1797551316	1332146220	1348919312	1826125402	63750	SRX22175831	SRS19233331	SRA1737851	South China University of Technology	South China University of Technology	2	0.90391	0.90473	0.3135	0.31222	0.83753	0.83613	0.53444	0.53443	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28612	28612	SRR26471891	SRX22175830	SRS19233328	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb wt eos 1	GSM7854239	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb wt eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854239	GSM7854239: cebpb wt eos 1; Danio rerio; RNA Seq	GSM7854239 r1	GSM7854239	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	Z1_1.fq.gz Z1_2.fq.gz	fastq fastq	6180805800.0	20602686.0	GSM7854239 r1	0:150 1:150	A:1699796929;C:1374020384;G:1377922189;T:1729003691;N:62607	150	150	1699796929	1374020384	1377922189	1729003691	62607	SRX22175830	SRS19233328	SRA1737851	South China University of Technology	South China University of Technology	2	0.91982	0.9224	0.18189	0.18148	0.82814	0.82672	0.51271	0.5152	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28613	28613	SRR26471892	SRX22175829	SRS19233330	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb wt eos 2	GSM7854240	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb wt eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854240	GSM7854240: cebpb wt eos 2; Danio rerio; RNA Seq	GSM7854240 r1	GSM7854240	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	Z2_1.fq.gz Z2_2.fq.gz	fastq fastq	6693470100.0	22311567.0	GSM7854240 r1	0:150 1:150	A:1840742978;C:1484923084;G:1499378237;T:1868364754;N:61047	150	150	1840742978	1484923084	1499378237	1868364754	61047	SRX22175829	SRS19233330	SRA1737851	South China University of Technology	South China University of Technology	2	0.92056	0.92353	0.18668	0.18721	0.82771	0.82696	0.53034	0.52277	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28614	28614	SRR26471893	SRX22175828	SRS19233332	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebpb mut eos 1	GSM7854237	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebpb mut eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:cebpb / \|transgene:Tgeslec:eGFP	GSM7854237	GSM7854237: cebpb mut eos 1; Danio rerio; RNA Seq	GSM7854237 r1	GSM7854237	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	F1_1.fq.gz F1_2.fq.gz	fastq fastq	7774783500.0	25915945.0	GSM7854237 r1	0:150 1:150	A:2205128515;C:1660071767;G:1677499789;T:2232048253;N:35176	150	150	2205128515	1660071767	1677499789	2232048253	35176	SRX22175828	SRS19233332	SRA1737851	South China University of Technology	South China University of Technology	2	0.90668	0.90886	0.34302	0.34395	0.81943	0.81937	0.5348	0.54523	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28615	28615	SRR26471894	SRX22175827	SRS19233329	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 wt eos 2	GSM7854236	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 wt eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854236	GSM7854236: cebp1 wt eos 2; Danio rerio; RNA Seq	GSM7854236 r1	GSM7854236	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	W2_1.fq.gz W2_2.fq.gz	fastq fastq	6478425300.0	21594751.0	GSM7854236 r1	0:150 1:150	A:2031706672;C:1135087913;G:1324534931;T:1987064653;N:31131	150	150	2031706672	1135087913	1324534931	1987064653	31131	SRX22175827	SRS19233329	SRA1737851	South China University of Technology	South China University of Technology	2	0.74912	0.74531	0.50454	0.49737	0.79255	0.78539	0.63484	0.64052	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28616	28616	SRR26471895	SRX22175826	SRS19233326	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 wt eos 1	GSM7854235	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 wt eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854235	GSM7854235: cebp1 wt eos 1; Danio rerio; RNA Seq	GSM7854235 r1	GSM7854235	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	W1_2.fq.gz W1_1.fq.gz	fastq fastq	6194437200.0	20648124.0	GSM7854235 r1	0:150 1:150	A:1953684038;C:1067667551;G:1247879965;T:1925172690;N:32956	150	150	1953684038	1067667551	1247879965	1925172690	32956	SRX22175826	SRS19233326	SRA1737851	South China University of Technology	South China University of Technology	2	0.76007	0.76295	0.54521	0.54298	0.78244	0.77281	0.62357	0.62562	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28617	28617	SRR26471896	SRX22175825	SRS19233327	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 mut eos 2	GSM7854234	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 mut eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP	GSM7854234	GSM7854234: cebp1 mut eos 2; Danio rerio; RNA Seq	GSM7854234 r1	GSM7854234	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	M2_2.fq.gz M2_1.fq.gz	fastq fastq	6104680800.0	20348936.0	GSM7854234 r1	0:150 1:150	A:1804058925;C:1198439018;G:1326225576;T:1775930488;N:26793	150	150	1804058925	1198439018	1326225576	1775930488	26793	SRX22175825	SRS19233327	SRA1737851	South China University of Technology	South China University of Technology	2	0.8123	0.81465	0.42735	0.42341	0.78171	0.77567	0.46764	0.65485	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
28618	28618	SRR26471897	SRX22175824	SRS19233325	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871	cebp1 mut eos 1	GSM7854233	source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 mut eos 1	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:cebp1 / \|transgene:Tgeslec:eGFP	GSM7854233	GSM7854233: cebp1 mut eos 1; Danio rerio; RNA Seq	GSM7854233 r1	GSM7854233	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467949	loader:fastq load.py	M1_1.fq.gz M1_2.fq.gz	fastq fastq	6409092000.0	21363640.0	GSM7854233 r1	0:150 1:150	A:1887432519;C:1294546709;G:1354360945;T:1872720156;N:31671	150	150	1887432519	1294546709	1354360945	1872720156	31671	SRX22175824	SRS19233325	SRA1737851	South China University of Technology	South China University of Technology	2	0.84504	0.84611	0.39473	0.39207	0.76319	0.75767	0.63936	0.62743	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures
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
30620	30620	SRR27907608	SRX23567386	SRS20412878	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591	KO12. Ctla 4 knockout	GSM8068839	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO12. Ctla 4 knockout	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068839	GSM8068839: KO12. Ctla 4 knockout; Danio rerio; RNA Seq	GSM8068839 r1	GSM8068839	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP488782	loader:fastq load.py	KO12_Clean_Data2.fq.gz KO12_Clean_Data1.fq.gz	fastq fastq	5415971621.0	18199812.0	GSM8068839 r1	0:148.79 1:148.79	A:1482389043;C:1213758088;G:1232295642;T:1487496355;N:32493	148	148	1482389043	1213758088	1232295642	1487496355	32493	SRX23567386	SRS20412878	SRA1799527	zhejiang university	zhejiang university	2	0.86496	0.86584	0.08493	0.08156	0.73553	0.73588	0.50941	0.5104	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30621	30621	SRR27907609	SRX23567385	SRS20412877	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591	KO11 Ctla 4 knockout	GSM8068838	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO11 Ctla 4 knockout	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068838	GSM8068838: KO11 Ctla 4 knockout; Danio rerio; RNA Seq	GSM8068838 r1	GSM8068838	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP488782	loader:fastq load.py	KO11_Clean_Data2.fq.gz KO11_Clean_Data1.fq.gz	fastq fastq	5443694370.0	18290488.0	GSM8068838 r1	0:148.81 1:148.81	A:1480267395;C:1230300897;G:1247791644;T:1485302181;N:32253	148	148	1480267395	1230300897	1247791644	1485302181	32253	SRX23567385	SRS20412877	SRA1799527	zhejiang university	zhejiang university	2	0.86445	0.86409	0.07094	0.06652	0.74738	0.74897	0.51339	0.51762	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30622	30622	SRR27907610	SRX23567384	SRS20412876	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591	KO9 Ctla 4 knockout	GSM8068837	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO\|geo loc name:missing\|collection date:missing	KO9 Ctla 4 knockout	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Ctla 4 KO	GSM8068837	GSM8068837: KO9 Ctla 4 knockout; Danio rerio; RNA Seq	GSM8068837 r1	GSM8068837	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP488782	loader:fastq load.py	KO9_Clean_Data2.fq.gz KO9_Clean_Data1.fq.gz	fastq fastq	5971590749.0	20072217.0	GSM8068837 r1	0:148.76 1:148.75	A:1640322573;C:1334570646;G:1352953128;T:1643708463;N:35939	148	148	1640322573	1334570646	1352953128	1643708463	35939	SRX23567384	SRS20412876	SRA1799527	zhejiang university	zhejiang university	2	0.86793	0.86937	0.07855	0.07588	0.74393	0.74523	0.50694	0.51104	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30623	30623	SRR27907611	SRX23567383	SRS20412875	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591	WT8 control	GSM8068836	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT8 control	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068836	GSM8068836: WT8 control; Danio rerio; RNA Seq	GSM8068836 r1	GSM8068836	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP488782	loader:fastq load.py	WT8_Clean_Data1.fq.gz WT8_Clean_Data2.fq.gz	fastq fastq	5740688401.0	19287992.0	GSM8068836 r1	0:148.82 1:148.81	A:1586419463;C:1274440057;G:1291660517;T:1588132746;N:35618	148	148	1586419463	1274440057	1291660517	1588132746	35618	SRX23567383	SRS20412875	SRA1799527	zhejiang university	zhejiang university	2	0.85516	0.85653	0.07987	0.07551	0.74515	0.74497	0.52575	0.52057	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30624	30624	SRR27907612	SRX23567382	SRS20412874	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591	WT7 control	GSM8068835	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT7 control	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068835	GSM8068835: WT7 control; Danio rerio; RNA Seq	GSM8068835 r1	GSM8068835	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP488782	loader:fastq load.py	WT7_Clean_Data2.fq.gz WT7_Clean_Data1.fq.gz	fastq fastq	5810188177.0	19521216.0	GSM8068835 r1	0:148.82 1:148.81	A:1609284873;C:1285068093;G:1302652710;T:1613147856;N:34645	148	148	1609284873	1285068093	1302652710	1613147856	34645	SRX23567382	SRS20412874	SRA1799527	zhejiang university	zhejiang university	2	0.83558	0.83684	0.08427	0.08011	0.75741	0.75836	0.52403	0.52405	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
30625	30625	SRR27907613	SRX23567381	SRS20412873	SRP488782	PRJNA1074407	Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq]	GSE255304	Transcriptome Analysis	Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		pubmed:40392591	WT1 control	GSM8068834	source name:intestine\|tissue:intestine\|cell type:leukocyte\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	WT1 control	The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	intestine		Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.		tissue:intestine\|cell type:leukocyte\|genotype:Wildtype	GSM8068834	GSM8068834: WT1 control; Danio rerio; RNA Seq	GSM8068834 r1	GSM8068834	1	Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP488782	loader:fastq load.py	WT1_Clean_Data2.fq.gz WT1_Clean_Data1.fq.gz	fastq fastq	5771161671.0	19396834.0	GSM8068834 r1	0:148.77 1:148.76	A:1593780869;C:1284499295;G:1300298518;T:1592548515;N:34474	148	148	1593780869	1284499295	1300298518	1592548515	34474	SRX23567381	SRS20412873	SRA1799527	zhejiang university	zhejiang university	2	0.85731	0.85944	0.0704	0.06703	0.76601	0.76607	0.53065	0.53445	149	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2024-02-07	Undetermined	Undetermined	Gut	Digestive System
31849	31849	SRR28735527	SRX24301508	SRS21065427	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970	stim2KO repllicate 3 RNASeq	GSM8215878	source name:eye\|tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf\|geo loc name:missing\|collection date:missing	stim2KO repllicate 3 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye		Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf	GSM8215878	GSM8215878: stim2KO repllicate 3 RNASeq; Danio rerio; RNA Seq	GSM8215878 r1	GSM8215878	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615	loader:fastq load.py	mut_rep_3_R1_001.fastq.gz mut_rep_3_R2_001.fastq.gz	fastq fastq	5198552618.0	25735409.0	GSM8215878 r1	0:101 1:101	A:1302884238;C:1298420335;G:1334893927;T:1262296331;N:57787	101	101	1302884238	1298420335	1334893927	1262296331	57787	SRX24301508	SRS21065427	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95719	0.95856	0.05756	0.05712	0.70534	0.70851	0.42046	0.41786	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31850	31850	SRR28735528	SRX24301507	SRS21065426	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970	stim2KO repllicate 2 RNASeq	GSM8215877	source name:eye\|tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf\|geo loc name:missing\|collection date:missing	stim2KO repllicate 2 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye		Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf	GSM8215877	GSM8215877: stim2KO repllicate 2 RNASeq; Danio rerio; RNA Seq	GSM8215877 r1	GSM8215877	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615	loader:fastq load.py	mut_rep_2_R1_001.fastq.gz mut_rep_2_R2_001.fastq.gz	fastq fastq	5641008570.0	27925785.0	GSM8215877 r1	0:101 1:101	A:1421655053;C:1399106135;G:1439454285;T:1380731092;N:62005	101	101	1421655053	1399106135	1439454285	1380731092	62005	SRX24301507	SRS21065426	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95794	0.9601	0.05457	0.05365	0.70942	0.71151	0.42408	0.42666	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31851	31851	SRR28735529	SRX24301506	SRS21065425	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970	stim2KO repllicate 1 RNASeq	GSM8215876	source name:eye\|tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye		Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		tissue:eye\|genotype:stim2a;stim2b / \|age:5 dpf	GSM8215876	GSM8215876: stim2KO repllicate 1 RNASeq; Danio rerio; RNA Seq	GSM8215876 r1	GSM8215876	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615	loader:fastq load.py	mut_rep_1_R1_001.fastq.gz mut_rep_1_R2_001.fastq.gz	fastq fastq	5147003026.0	25480213.0	GSM8215876 r1	0:101 1:101	A:1302966446;C:1274828722;G:1325578656;T:1243571921;N:57281	101	101	1302966446	1274828722	1325578656	1243571921	57281	SRX24301506	SRS21065425	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95963	0.96036	0.05042	0.05053	0.71275	0.71725	0.41458	0.41703	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31852	31852	SRR28735530	SRX24301505	SRS21065424	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970	Tg repllicate 3 RNASeq	GSM8215875	source name:eye\|tissue:eye\|genotype:AB\|age:5 dpf\|geo loc name:missing\|collection date:missing	Tg repllicate 3 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye		Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		tissue:eye\|genotype:AB\|age:5 dpf	GSM8215875	GSM8215875: Tg repllicate 3 RNASeq; Danio rerio; RNA Seq	GSM8215875 r1	GSM8215875	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615	loader:fastq load.py	wt_rep_3_R1_001.fastq.gz wt_rep_3_R2_001.fastq.gz	fastq fastq	4648345422.0	23011611.0	GSM8215875 r1	0:101 1:101	A:1186641846;C:1144216110;G:1192801277;T:1124633797;N:52392	101	101	1186641846	1144216110	1192801277	1124633797	52392	SRX24301505	SRS21065424	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.9575	0.95756	0.05359	0.05311	0.69875	0.70315	0.42041	0.41054	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31853	31853	SRR28735531	SRX24301504	SRS21065423	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970	Tg repllicate 2 RNASeq	GSM8215874	source name:eye\|tissue:eye\|genotype:AB\|age:5 dpf\|geo loc name:missing\|collection date:missing	Tg repllicate 2 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye		Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		tissue:eye\|genotype:AB\|age:5 dpf	GSM8215874	GSM8215874: Tg repllicate 2 RNASeq; Danio rerio; RNA Seq	GSM8215874 r1	GSM8215874	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615	loader:fastq load.py	wt_rep_2_R1_001.fastq.gz wt_rep_2_R2_001.fastq.gz	fastq fastq	4769618546.0	23611973.0	GSM8215874 r1	0:101 1:101	A:1218890346;C:1171831021;G:1228410692;T:1150434539;N:51948	101	101	1218890346	1171831021	1228410692	1150434539	51948	SRX24301504	SRS21065423	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95682	0.95517	0.05192	0.05059	0.70849	0.71543	0.41181	0.41549	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
31854	31854	SRR28735532	SRX24301503	SRS21065422	SRP502615	PRJNA1101945	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]	GSE264309	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons. The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: AB and double knockout for stim2 stim2a;stim2b / zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.	parent bioproject:PRJNA1101942	pubmed:39424970	Tg repllicate 1 RNASeq	GSM8215873	source name:eye\|tissue:eye\|genotype:AB\|age:5 dpf\|geo loc name:missing\|collection date:missing	Tg repllicate 1 RNASeq	Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17 Illumina and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a StringTie version 1.3.3b and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment transcript assembly and quantification for each replicate and differential gene expression analysis respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample	eye		Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer’s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.		tissue:eye\|genotype:AB\|age:5 dpf	GSM8215873	GSM8215873: Tg repllicate 1 RNASeq; Danio rerio; RNA Seq	GSM8215873 r1	GSM8215873	1	Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260 280 and 230 nm and Bioanalyzer Nano RNA chip Agilent USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research Irvine CA USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP502615	loader:fastq load.py	wt_rep_1_R1_001.fastq.gz wt_rep_1_R2_001.fastq.gz	fastq fastq	4771981138.0	23623669.0	GSM8215873 r1	0:101 1:101	A:1222918015;C:1171619846;G:1231393968;T:1145997219;N:52090	101	101	1222918015	1171619846	1231393968	1145997219	52090	SRX24301503	SRS21065422	SRA1848589	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.95739	0.95621	0.05362	0.0539	0.71301	0.71979	0.42337	0.40836	101	101	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Poland	2024-04-18	Larval	Larval	Eye	Sensory System
34987	34987	SRR32942209	SRX28216558	SRS24541720	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial uninjured heart	strain:not applicable\|dev stage:uninjured\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial uninjured heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400023364BR L01 read.T1 C1.part 004	DP8400023364BR L01 read.T1 C1.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400023364BR_L01_read.part_004_1.fq.gz DP8400023364BR_L01_read.part_004_2.fq.gz	fastq fastq	123077427480.0	911684648.0	DP8400023364BR L01 read.part 004 1.fq.gz										SRX28216558	SRS24541720	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34988	34988	SRR32942163	SRX28216557	SRS24541723	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 14 dpa heart	strain:not applicable\|dev stage:14 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 14 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400023362BR L01 read.T7 C2.part 004	DP8400023362BR L01 read.T7 C2.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400023362BR_L01_read.part_004_1.fq.gz DP8400023362BR_L01_read.part_004_2.fq.gz	fastq fastq	107293454415.0	794766329.0	DP8400023362BR L01 read.part 004 1.fq.gz	0:35 1:100	A:31376398573;C:25690917149;G:24154317375;T:26069613878;N:2207440	35	100	31376398573	25690917149	24154317375	26069613878	2207440	SRX28216557	SRS24541723	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34989	34989	SRR32942164	SRX28216556	SRS24541723	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 14 dpa heart	strain:not applicable\|dev stage:14 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 14 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400023361BR L01 read.T7 C1.part 004	DP8400023361BR L01 read.T7 C1.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400023361BR_L01_read.part_004_1.fq.gz DP8400023361BR_L01_read.part_004_2.fq.gz	fastq fastq	73541011590.0	544748234.0	DP8400023361BR L01 read.part 004 1.fq.gz	0:35 1:100	A:21245841948;C:17695592198;G:16579296946;T:18018318788;N:1961710	35	100	21245841948	17695592198	16579296946	18018318788	1961710	SRX28216556	SRS24541723	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34990	34990	SRR32942165	SRX28216555	SRS24507277	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 3D heart	strain:not applicable\|dev stage:uninjured\|collection date:2021 02\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 3D heart\|BioSampleModel:Model organism or animal									Stereo seq of 3D zebrafish heart	DP8400018806BL L01 read.DP8400016191TL D2.part 004	DP8400018806BL L01 read.DP8400016191TL D2.part 004	Stereo seq of 3D zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400018806BL_L01_read.part_004_1.fq.gz DP8400018806BL_L01_read.part_004_2.fq.gz	fastq fastq	55082417580.0	408017908.0	DP8400018806BL L01 read.part 004 1.fq.gz	0:35 1:100	A:13778227671;C:14713292408;G:13807456331;T:12779522494;N:3918676	35	100	13778227671	14713292408	13807456331	12779522494	3918676	SRX28216555	SRS24507277	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34991	34991	SRR32942166	SRX28216554	SRS24541719	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 28 dpa heart	strain:not applicable\|dev stage:28 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 28 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022484TL L01 read.T8 C3.part 004	DP8400022484TL L01 read.T8 C3.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022484TL_L01_read.part_004_1.fq.gz DP8400022484TL_L01_read.part_004_2.fq.gz	fastq fastq	132532472295.0	981722017.0	DP8400022484TL L01 read.part 004 1.fq.gz										SRX28216554	SRS24541719	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34992	34992	SRR32942167	SRX28216553	SRS24541721	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 3 dpa heart	strain:not applicable\|dev stage:3 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 3 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022389BL L01 read.T5 C2.part 004	DP8400022389BL L01 read.T5 C2.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022389BL_L01_read.part_004_1.fq.gz DP8400022389BL_L01_read.part_004_2.fq.gz	fastq fastq	104447005335.0	773681521.0	DP8400022389BL L01 read.part 004 1.fq.gz	0:35 1:100	A:27343177960;C:27134625733;G:25518535252;T:24448625683;N:2040707	35	100	27343177960	27134625733	25518535252	24448625683	2040707	SRX28216553	SRS24541721	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34993	34993	SRR32942168	SRX28216552	SRS24541722	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 6 hpa heart	strain:not applicable\|dev stage:6 hpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 6 hpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022386BL L01 read.T2 C1.part 004	DP8400022386BL L01 read.T2 C1.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022386BL_L01_read.part_004_1.fq.gz DP8400022386BL_L01_read.part_004_2.fq.gz	fastq fastq	133549992405.0	989259203.0	DP8400022386BL L01 read.part 004 1.fq.gz										SRX28216552	SRS24541722	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34994	34994	SRR32942169	SRX28216551	SRS24541717	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 1 dpa heart	strain:not applicable\|dev stage:1 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 1 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022382TR L01 read.T4 C1.part 004	DP8400022382TR L01 read.T4 C1.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022382TR_L01_read.part_004_1.fq.gz DP8400022382TR_L01_read.part_004_2.fq.gz	fastq fastq	117481461480.0	870233048.0	DP8400022382TR L01 read.part 004 1.fq.gz										SRX28216551	SRS24541717	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34995	34995	SRR32942170	SRX28216550	SRS24541717	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 1 dpa heart	strain:not applicable\|dev stage:1 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 1 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022381TR L01 read.T4 C2.part 004	DP8400022381TR L01 read.T4 C2.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022381TR_L01_read.part_004_1.fq.gz DP8400022381TR_L01_read.part_004_2.fq.gz	fastq fastq	115488770760.0	855472376.0	DP8400022381TR L01 read.part 004 1.fq.gz										SRX28216550	SRS24541717	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34996	34996	SRR32942171	SRX28216549	SRS24541722	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 6 hpa heart	strain:not applicable\|dev stage:6 hpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 6 hpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022380TR L01 read.T2 C2.part 004	DP8400022380TR L01 read.T2 C2.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022380TR_L01_read.part_004_1.fq.gz DP8400022380TR_L01_read.part_004_2.fq.gz	fastq fastq	113741885745.0	842532487.0	DP8400022380TR L01 read.part 004 1.fq.gz										SRX28216549	SRS24541722	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34997	34997	SRR32942172	SRX28216548	SRS24541722	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 6 hpa heart	strain:not applicable\|dev stage:6 hpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 6 hpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022379TR L01 read.T2 C3.part 004	DP8400022379TR L01 read.T2 C3.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022379TR_L01_read.part_004_1.fq.gz DP8400022379TR_L01_read.part_004_2.fq.gz	fastq fastq	122405973930.0	906710918.0	DP8400022379TR L01 read.part 004 1.fq.gz										SRX28216548	SRS24541722	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34998	34998	SRR32942173	SRX28216547	SRS24541721	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 3 dpa heart	strain:not applicable\|dev stage:3 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 3 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022378TR L01 read.T5 C1.part 004	DP8400022378TR L01 read.T5 C1.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022378TR_L01_read.part_004_1.fq.gz DP8400022378TR_L01_read.part_004_2.fq.gz	fastq fastq	111214895535.0	823814041.0	DP8400022378TR L01 read.part 004 1.fq.gz										SRX28216547	SRS24541721	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
34999	34999	SRR32942174	SRX28216546	SRS24541718	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 7 dpa heart	strain:not applicable\|dev stage:7 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 7 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022137TL L01 read.T6 C2.part 004	DP8400022137TL L01 read.T6 C2.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022137TL_L01_read.part_004_1.fq.gz DP8400022137TL_L01_read.part_004_2.fq.gz	fastq fastq	119483176815.0	885060569.0	DP8400022137TL L01 read.part 004 1.fq.gz										SRX28216546	SRS24541718	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
35000	35000	SRR32942175	SRX28216545	SRS24541718	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 7 dpa heart	strain:not applicable\|dev stage:7 dpa\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 7 dpa heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022136TL L01 read.T6 C1.part 004	DP8400022136TL L01 read.T6 C1.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022136TL_L01_read.part_004_1.fq.gz DP8400022136TL_L01_read.part_004_2.fq.gz	fastq fastq	129016315215.0	955676409.0	DP8400022136TL L01 read.part 004 1.fq.gz										SRX28216545	SRS24541718	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
35001	35001	SRR32942176	SRX28216544	SRS24507277	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial 3D heart	strain:not applicable\|dev stage:uninjured\|collection date:2021 02\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial 3D heart\|BioSampleModel:Model organism or animal									Stereo seq of 3D zebrafish heart	DP8400018805BL L01 read.DP8400016191TL D3.part 004	DP8400018805BL L01 read.DP8400016191TL D3.part 004	Stereo seq of 3D zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400018805BL_L01_read.part_004_1.fq.gz DP8400018805BL_L01_read.part_004_2.fq.gz	fastq fastq	61237875690.0	453613894.0	DP8400018805BL L01 read.part 004 1.fq.gz	0:35 1:100	A:15070939100;C:16649524218;G:15610652660;T:13904423716;N:2335996	35	100	15070939100	16649524218	15610652660	13904423716	2335996	SRX28216544	SRS24507277	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular System
35002	35002	SRR32942177	SRX28216543	SRS24541720	SRP573401	PRJNA1233465	An Organ wide Spatiotemporal Transcriptomic and Cellular Atlas of the Regenerating Zebrafish Heart	PRJNA1233465	Other	Adult zebrafish robustly regenerate injured hearts through a complex orchestration of various cell types and a multitude of molecules. Here we utilize single cell RNA sequencing scRNA seq and Stereo seq to construct a spatially resolved cell dataset of regenerating zebrafish hearts across eight time points.				spatial uninjured heart	strain:not applicable\|dev stage:uninjured\|collection date:2021 08\|geo loc name:China:Qingdao\|sex:not applicable\|tissue:heart\|isolation source:spatial uninjured heart\|BioSampleModel:Model organism or animal									Stereo seq of zebrafish heart	DP8400022030BR L01 read.T1 C3.part 004	DP8400022030BR L01 read.T1 C3.part 004	Stereo seq of zebrafish heart		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP573401		DP8400022030BR_L01_read.part_004_1.fq.gz DP8400022030BR_L01_read.part_004_2.fq.gz	fastq fastq	109611340155.0	811935853.0	DP8400022030BR L01 read.part 004 1.fq.gz										SRX28216543	SRS24541720	SRA2105098	BGI Research	BGI Research Institute of Evolution and Marine Biodiversity, Ocean University of China												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2025-04-02	Undetermined	Adult	Heart	Cardiovascular 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");;