metadata: run_metadata: 68 rows where experiment.library_layout = "PAIRED", technology = "generic-scrnaseq-only" and tissue

68 rows where experiment.library_layout = "PAIRED", technology = "generic-scrnaseq-only" and tissue_curation = "Tail"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	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
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
64447	64447	SRR14703445	SRX11041466	SRS9110394	SRP322195	PRJNA734348	Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs	GSE175951	Other	Unlike that of mammals the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles the zygotic mutant zebrafish of dnmt1 the major DNA methylation maintenance methyltransferase surprisingly can develop to term. To solve the role of DNA methylation in early development we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers which acquire ectopic H3K27ac accessible chromatin and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast embryonic enhancers are generally CG poor methylation insensitive and are bound by CG less TFs. Hence the global DNA methylome inheritance is essential for vertebrate early development and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq total RNA seq scRNA seq CUT&RUN ChIP seq and ATAC seq in control and dnmt1 mKD embryos at oocyt…	pubmed:34936444	5dpf tail dnmt1 zKO total RNA seq rep2	GSM5351821	source name:larva\|strain:TL\|genotype:dnmt1 / \|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	5dpf tail dnmt1 zKO total RNA seq rep2	All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al. 2013 with the following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al. 2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10 transcript counting and gene cell barcode matrix generation. Before the downstream analysis cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 L…	larva	Embryos at 5 dpf were euthanized with tricaine and tail was dissected carefully by tweezers. post brief grinding tissues froze at 80℃ for later usage.	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.	The dnmt1 mutant TL strain was used in the experiments. The adult fish were fed with live adult brine shrimp in the morning and evening. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al. 1995.	strain:TL\|genotype:dnmt1 / \|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	GSM5351821	GSM5351821: 5dpf tail dnmt1 zKO total RNA seq rep2; Danio rerio; RNA Seq	GSM5351821		1	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351821	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	5dpf_tail_dnmt1_zKO_total_RNA_seq_rep2_r1.fq.gz 5dpf_tail_dnmt1_zKO_total_RNA_seq_rep2_r2.fq.gz	fastq fastq	12390971100.0	41303237.0	GSM5351821 r1	0:150 1:150	A:3159992851;C:3017116837;G:3080231294;T:3133156041;N:474077	150	150	3159992851	3017116837	3080231294	3133156041	474077	SRX11041466	SRS9110394	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.93558	0.94895	0.11597	0.11647	0.71041	0.71403	0.45173	0.45741	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2021-06-01	Larval	Larval	Tail	Multi-system
64448	64448	SRR14703444	SRX11041465	SRS9110393	SRP322195	PRJNA734348	Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs	GSE175951	Other	Unlike that of mammals the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles the zygotic mutant zebrafish of dnmt1 the major DNA methylation maintenance methyltransferase surprisingly can develop to term. To solve the role of DNA methylation in early development we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers which acquire ectopic H3K27ac accessible chromatin and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast embryonic enhancers are generally CG poor methylation insensitive and are bound by CG less TFs. Hence the global DNA methylome inheritance is essential for vertebrate early development and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq total RNA seq scRNA seq CUT&RUN ChIP seq and ATAC seq in control and dnmt1 mKD embryos at oocyt…	pubmed:34936444	5dpf tail dnmt1 zKO total RNA seq rep1	GSM5351820	source name:larva\|strain:TL\|genotype:dnmt1 / \|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	5dpf tail dnmt1 zKO total RNA seq rep1	All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al. 2013 with the following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al. 2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10 transcript counting and gene cell barcode matrix generation. Before the downstream analysis cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 L…	larva	Embryos at 5 dpf were euthanized with tricaine and tail was dissected carefully by tweezers. post brief grinding tissues froze at 80℃ for later usage.	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.	The dnmt1 mutant TL strain was used in the experiments. The adult fish were fed with live adult brine shrimp in the morning and evening. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al. 1995.	strain:TL\|genotype:dnmt1 / \|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	GSM5351820	GSM5351820: 5dpf tail dnmt1 zKO total RNA seq rep1; Danio rerio; RNA Seq	GSM5351820		1	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351820	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	5dpf_tail_dnmt1_zKO_total_RNA_seq_rep1_r1.fq.gz 5dpf_tail_dnmt1_zKO_total_RNA_seq_rep1_r2.fq.gz	fastq fastq	6710727000.0	22369090.0	GSM5351820 r1	0:150 1:150	A:1321771844;C:2028485839;G:2067617742;T:1292662830;N:188745	150	150	1321771844	2028485839	2067617742	1292662830	188745	SRX11041465	SRS9110393	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.34696	0.3428	0.09476	0.09314	0.83918	0.84756	0.62449	0.61549	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2021-06-01	Larval	Larval	Tail	Multi-system
64449	64449	SRR14703443	SRX11041464	SRS9110392	SRP322195	PRJNA734348	Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs	GSE175951	Other	Unlike that of mammals the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles the zygotic mutant zebrafish of dnmt1 the major DNA methylation maintenance methyltransferase surprisingly can develop to term. To solve the role of DNA methylation in early development we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers which acquire ectopic H3K27ac accessible chromatin and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast embryonic enhancers are generally CG poor methylation insensitive and are bound by CG less TFs. Hence the global DNA methylome inheritance is essential for vertebrate early development and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq total RNA seq scRNA seq CUT&RUN ChIP seq and ATAC seq in control and dnmt1 mKD embryos at oocyt…	pubmed:34936444	5dpf tail WT total RNA seq rep2	GSM5351819	source name:larva\|strain:TL\|genotype:WT\|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	5dpf tail WT total RNA seq rep2	All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al. 2013 with the following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al. 2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10 transcript counting and gene cell barcode matrix generation. Before the downstream analysis cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 L…	larva	Embryos at 5 dpf were euthanized with tricaine and tail was dissected carefully by tweezers. post brief grinding tissues froze at 80℃ for later usage.	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.	The wild type TL strain was used in the experiments. The adult fish were fed with live adult brine shrimp in the morning and evening. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al. 1995.	strain:TL\|genotype:WT\|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	GSM5351819	GSM5351819: 5dpf tail WT total RNA seq rep2; Danio rerio; RNA Seq	GSM5351819		1	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351819	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	5dpf_tail_WT_total_RNA_seq_rep2_r1.fq.gz 5dpf_tail_WT_total_RNA_seq_rep2_r2.fq.gz	fastq fastq	12867167700.0	42890559.0	GSM5351819 r1	0:150 1:150	A:3272676564;C:3140399740;G:3207545913;T:3246051753;N:493730	150	150	3272676564	3140399740	3207545913	3246051753	493730	SRX11041464	SRS9110392	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.93767	0.95319	0.10862	0.10917	0.71104	0.71445	0.44955	0.44841	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2021-06-01	Larval	Larval	Tail	Multi-system
64450	64450	SRR14703442	SRX11041463	SRS9110390	SRP322195	PRJNA734348	Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs	GSE175951	Other	Unlike that of mammals the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles the zygotic mutant zebrafish of dnmt1 the major DNA methylation maintenance methyltransferase surprisingly can develop to term. To solve the role of DNA methylation in early development we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers which acquire ectopic H3K27ac accessible chromatin and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast embryonic enhancers are generally CG poor methylation insensitive and are bound by CG less TFs. Hence the global DNA methylome inheritance is essential for vertebrate early development and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq total RNA seq scRNA seq CUT&RUN ChIP seq and ATAC seq in control and dnmt1 mKD embryos at oocyt…	pubmed:34936444	5dpf tail WT total RNA seq rep1	GSM5351818	source name:larva\|strain:TL\|genotype:WT\|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	5dpf tail WT total RNA seq rep1	All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al. 2013 with the following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al. 2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10 transcript counting and gene cell barcode matrix generation. Before the downstream analysis cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 L…	larva	Embryos at 5 dpf were euthanized with tricaine and tail was dissected carefully by tweezers. post brief grinding tissues froze at 80℃ for later usage.	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.	The wild type TL strain was used in the experiments. The adult fish were fed with live adult brine shrimp in the morning and evening. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al. 1995.	strain:TL\|genotype:WT\|developmental stage:5dpf\|tissue:larva tail\|treatment:untreated	GSM5351818	GSM5351818: 5dpf tail WT total RNA seq rep1; Danio rerio; RNA Seq	GSM5351818		1	The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen Cat A33248 and spun at 14 000 rpm for 15 min. Next the top phase was taken out from the tube added 1 µl LPA Sigma Cat 56575 and mixed well using pipettes. Then RNA was precipitated by adding 750 µl isopropanol Sigma Cat 59304 at 20℃ overnight. At next day the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol re suspend in 20 µl RNase free water and stored at 80℃ for later usage. NEBNext rRNA Depletion Kit NEB Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly rRNA were hybridized with probes and digested with RNase H then excess probes were digested with DNase I. post that NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB Cat E7771S and second strand synthesis modules NEB Cat E7550S then purified with Ampure XP beads Beckman Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB Cat E7645S. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351818	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	5dpf_tail_WT_total_RNA_seq_rep1_r1.fq.gz 5dpf_tail_WT_total_RNA_seq_rep1_r2.fq.gz	fastq fastq	6865936800.0	22886456.0	GSM5351818 r1	0:150 1:150	A:1312171184;C:2122611322;G:2164809991;T:1266152354;N:191949	150	150	1312171184	2122611322	2164809991	1266152354	191949	SRX11041463	SRS9110390	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.23917	0.24637	0.04793	0.04901	0.898	0.90585	0.68896	0.67741	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2021-06-01	Larval	Larval	Tail	Multi-system

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