run_metadata
84 rows where experiment.library_selection = "cDNA", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "Multi-system"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 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 | |||||||||
| 60001 | 60001 | SRR12083659 | SRX8610753 | SRS6900398 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a High TFC 3 | GSM4635496 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a High mKO2 High | Pax2a High TFC 3 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a High mKO2 High | GSM4635496 | GSM4635496: Pax2a High TFC 3; Danio rerio; RNA Seq | GSM4635496 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635496 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-highset3_S14_R1_001.fastq.gz Pax2a-highset3_S14_R2_001.fastq.gz | fastq fastq | 16108716672.0 | 80176158.0 | GSM4635496 r1 | 0:100.44 1:100.48 | A:4075320644;C:4124512580;G:3756402856;T:4151374263;N:1106329 | 100 | 100 | 4075320644 | 4124512580 | 3756402856 | 4151374263 | 1106329 | SRX8610753 | SRS6900398 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.53855 | 0.55508 | 0.21647 | 0.22708 | 0.82775 | 0.82838 | 0.43125 | 0.42144 | 101 | 100 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||
| 60002 | 60002 | SRR12083658 | SRX8610752 | SRS6900397 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a Low TFC 3 | GSM4635495 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | Pax2a Low TFC 3 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | GSM4635495 | GSM4635495: Pax2a Low TFC 3; Danio rerio; RNA Seq | GSM4635495 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635495 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-lowset3_S13_R2_001.fastq.gz Pax2a-lowset3_S13_R1_001.fastq.gz | fastq fastq | 15927464315.0 | 79263861.0 | GSM4635495 r1 | 0:100.42 1:100.53 | A:3806928663;C:4340989624;G:3919724503;T:3858828310;N:993215 | 100 | 100 | 3806928663 | 4340989624 | 3919724503 | 3858828310 | 993215 | SRX8610752 | SRS6900397 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.18449 | 0.18221 | 0.07867 | 0.07638 | 0.91488 | 0.91419 | 0.61183 | 0.60137 | 100 | 101 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||
| 60003 | 60003 | SRR12083657 | SRX8610751 | SRS6900396 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a High TFC 2 | GSM4635494 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a High mKO2 High | Pax2a High TFC 2 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a High mKO2 High | GSM4635494 | GSM4635494: Pax2a High TFC 2; Danio rerio; RNA Seq | GSM4635494 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635494 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-highset2_S12_R1_001.fastq.gz Pax2a-highset2_S12_R2_001.fastq.gz | fastq fastq | 15523399241.0 | 77253456.0 | GSM4635494 r1 | 0:100.43 1:100.51 | A:3874954294;C:4043105713;G:3665233417;T:3939083016;N:1022801 | 100 | 100 | 3874954294 | 4043105713 | 3665233417 | 3939083016 | 1022801 | SRX8610751 | SRS6900396 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.33224 | 0.33308 | 0.1301 | 0.13243 | 0.87411 | 0.8732 | 0.45849 | 0.46552 | 101 | 101 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||
| 60004 | 60004 | SRR12083656 | SRX8610750 | SRS6900395 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a Low TFC 2 | GSM4635493 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | Pax2a Low TFC 2 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | GSM4635493 | GSM4635493: Pax2a Low TFC 2; Danio rerio; RNA Seq | GSM4635493 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635493 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-lowset2_S11_R2_001.fastq.gz Pax2a-lowset2_S11_R1_001.fastq | fastq fastq | 14562196360.0 | 85940573.0 | GSM4635493 r1 | 0:100.38 1:100.53 | A:3643644077;C:3784618122;G:3352785620;T:3780129729;N:1018812 | 100 | 100 | 3643644077 | 3784618122 | 3352785620 | 3780129729 | 1018812 | SRX8610750 | SRS6900395 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.16299 | 0.15776 | 0.06375 | 0.06201 | 0.93162 | 0.93117 | 0.63175 | 0.62162 | 101 | 101 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||
| 60005 | 60005 | SRR12083655 | SRX8610749 | SRS6900394 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a High TFC 1 | GSM4635492 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a High mKO2 High | Pax2a High TFC 1 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a High mKO2 High | GSM4635492 | GSM4635492: Pax2a High TFC 1; Danio rerio; RNA Seq | GSM4635492 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635492 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-highset1_S10_R1_001.fastq.gz Pax2a-highset1_S10_R2_001.fastq.gz | fastq fastq | 16402884907.0 | 81622449.0 | GSM4635492 r1 | 0:100.45 1:100.51 | A:4148895557;C:4226508291;G:3782541016;T:4243916995;N:1023048 | 100 | 100 | 4148895557 | 4226508291 | 3782541016 | 4243916995 | 1023048 | SRX8610749 | SRS6900394 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.25304 | 0.25554 | 0.09753 | 0.10045 | 0.89986 | 0.89936 | 0.4275 | 0.41328 | 101 | 99 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||
| 60006 | 60006 | SRR12083654 | SRX8610748 | SRS6900393 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a Low TFC 1 | GSM4635491 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | Pax2a Low TFC 1 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | GSM4635491 | GSM4635491: Pax2a Low TFC 1; Danio rerio; RNA Seq | GSM4635491 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635491 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-lowset1_S9_R1_001.fastq.gz Pax2a-lowset1_S9_R2_001.fastq.gz | fastq fastq | 17841813800.0 | 88772569.0 | GSM4635491 r1 | 0:100.47 1:100.51 | A:4653492569;C:4489464840;G:4023148591;T:4674617491;N:1090309 | 100 | 100 | 4653492569 | 4489464840 | 4023148591 | 4674617491 | 1090309 | SRX8610748 | SRS6900393 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.08055 | 0.07962 | 0.02812 | 0.02691 | 0.96126 | 0.96126 | 0.67769 | 0.72985 | 100 | 101 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | 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 | |||||||||
| 68079 | 68079 | SRR17604930 | SRX13773746 | SRS11653747 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt Ctrl rep3 | GSM5814820 | tissue:epithelial|age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | Krt Ctrl rep3 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814820 | GSM5814820: Krt Ctrl rep3; Danio rerio; RNA Seq | GSM5814820 r1 | GSM5814820 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | D9_AAGAGG_L007_R1_001.fastq.gz | fastq | 1119889717.0 | 11088017.0 | GSM5814820 r1 | 0:101 1:0 | A:268013821;C:268948711;G:354482020;T:228355242;N:89923 | 101 | 0 | 268013821 | 268948711 | 354482020 | 228355242 | 89923 | SRX13773746 | SRS11653747 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.83634 | 0.25142 | 0.92107 | 0.73967 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68080 | 68080 | SRR17604931 | SRX13773746 | SRS11653747 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt Ctrl rep3 | GSM5814820 | tissue:epithelial|age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | Krt Ctrl rep3 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:3|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814820 | GSM5814820: Krt Ctrl rep3; Danio rerio; RNA Seq | GSM5814820 r1 | GSM5814820 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | D9_AAGAGG_L008_R1_001.fastq.gz | fastq | 1107311076.0 | 10963476.0 | GSM5814820 r2 | 0:101 1:0 | A:265076502;C:265784761;G:350224779;T:226169505;N:55529 | 101 | 0 | 265076502 | 265784761 | 350224779 | 226169505 | 55529 | SRX13773746 | SRS11653747 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.83676 | 0.25471 | 0.92172 | 0.75036 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68085 | 68085 | SRR17604936 | SRX13773743 | SRS11653744 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt V12 rep3 | GSM5814817 | tissue:epithelial|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | Krt V12 rep3 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814817 | GSM5814817: Krt V12 rep3; Danio rerio; RNA Seq | GSM5814817 r1 | GSM5814817 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | d12_GAGTCA_L007_R1_001.fastq.gz | fastq | 1293081083.0 | 12802783.0 | GSM5814817 r1 | 0:101 1:0 | A:294765651;C:315869756;G:422506461;T:259837016;N:102199 | 101 | 0 | 294765651 | 315869756 | 422506461 | 259837016 | 102199 | SRX13773743 | SRS11653744 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.86334 | 0.24183 | 0.8915 | 0.71576 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68086 | 68086 | SRR17604937 | SRX13773743 | SRS11653744 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt V12 rep3 | GSM5814817 | tissue:epithelial|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | Krt V12 rep3 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814817 | GSM5814817: Krt V12 rep3; Danio rerio; RNA Seq | GSM5814817 r1 | GSM5814817 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | d12_GAGTCA_L008_R1_001.fastq.gz | fastq | 1275303871.0 | 12626771.0 | GSM5814817 r2 | 0:101 1:0 | A:290705038;C:311345036;G:416458015;T:256730885;N:64897 | 101 | 0 | 290705038 | 311345036 | 416458015 | 256730885 | 64897 | SRX13773743 | SRS11653744 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.86353 | 0.24248 | 0.89025 | 0.73082 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68091 | 68091 | SRR17604942 | SRX13773740 | SRS11653741 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt Ctrl rep2 | GSM5814814 | tissue:epithelial|age:3dpf|batch:2|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | Krt Ctrl rep2 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:2|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814814 | GSM5814814: Krt Ctrl rep2; Danio rerio; RNA Seq | GSM5814814 r1 | GSM5814814 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | C9_AAGCCT_L007_R1_001.fastq.gz | fastq | 2009406817.0 | 19895117.0 | GSM5814814 r1 | 0:101 1:0 | A:438640008;C:494033974;G:682135581;T:394568602;N:28652 | 101 | 0 | 438640008 | 494033974 | 682135581 | 394568602 | 28652 | SRX13773740 | SRS11653741 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.88893 | 0.24477 | 0.94992 | 0.77184 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68094 | 68094 | SRR17604945 | SRX13773737 | SRS11653738 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt V12 rep2 | GSM5814811 | tissue:epithelial|age:3dpf|batch:2|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | Krt V12 rep2 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:2|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814811 | GSM5814811: Krt V12 rep2; Danio rerio; RNA Seq | GSM5814811 r1 | GSM5814811 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | C12_GGAGAA_L007_R1_001.fastq.gz | fastq | 2120385617.0 | 20993917.0 | GSM5814811 r1 | 0:101 1:0 | A:468255703;C:520073226;G:720772615;T:411253641;N:30432 | 101 | 0 | 468255703 | 520073226 | 720772615 | 411253641 | 30432 | SRX13773737 | SRS11653738 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.89927 | 0.21831 | 0.95373 | 0.71636 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68097 | 68097 | SRR17604948 | SRX13773734 | SRS11653735 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt Ctrl rep1 | GSM5814808 | tissue:epithelial|age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | Krt Ctrl rep1 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814808 | GSM5814808: Krt Ctrl rep1; Danio rerio; RNA Seq | GSM5814808 r1 | GSM5814808 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | B9_ACCTCA_L003_R1_001.fastq.gz | fastq | 1085863625.0 | 10751125.0 | GSM5814808 r1 | 0:101 1:0 | A:228925069;C:268633161;G:378723631;T:209535574;N:46190 | 101 | 0 | 228925069 | 268633161 | 378723631 | 209535574 | 46190 | SRX13773734 | SRS11653735 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.9347 | 0.22992 | 0.93779 | 0.72855 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68098 | 68098 | SRR17604949 | SRX13773734 | SRS11653735 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt Ctrl rep1 | GSM5814808 | tissue:epithelial|age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | Krt Ctrl rep1 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814808 | GSM5814808: Krt Ctrl rep1; Danio rerio; RNA Seq | GSM5814808 r1 | GSM5814808 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | B9_ACCTCA_L004_R1_001.fastq.gz | fastq | 1094625173.0 | 10837873.0 | GSM5814808 r2 | 0:101 1:0 | A:230674174;C:270764802;G:381635055;T:211445587;N:105555 | 101 | 0 | 230674174 | 270764802 | 381635055 | 211445587 | 105555 | SRX13773734 | SRS11653735 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.93399 | 0.22867 | 0.93774 | 0.75465 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68103 | 68103 | SRR17604954 | SRX13773731 | SRS11653732 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt V12 rep1 | GSM5814805 | tissue:epithelial|age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | Krt V12 rep1 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814805 | GSM5814805: Krt V12 rep1; Danio rerio; RNA Seq | GSM5814805 r1 | GSM5814805 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | B12_GTCGTA_L003_R1_001.fastq.gz | fastq | 1279886443.0 | 12672143.0 | GSM5814805 r1 | 0:101 1:0 | A:287939360;C:312300654;G:420407313;T:259182902;N:56214 | 101 | 0 | 287939360 | 312300654 | 420407313 | 259182902 | 56214 | SRX13773731 | SRS11653732 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.89701 | 0.22936 | 0.9275 | 0.76668 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system | |||||||||||||||||
| 68104 | 68104 | SRR17604955 | SRX13773731 | SRS11653732 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt V12 rep1 | GSM5814805 | tissue:epithelial|age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | Krt V12 rep1 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:1|genotype:mutant HRas G12V|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814805 | GSM5814805: Krt V12 rep1; Danio rerio; RNA Seq | GSM5814805 r1 | GSM5814805 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | B12_GTCGTA_L004_R1_001.fastq.gz | fastq | 1292551237.0 | 12797537.0 | GSM5814805 r2 | 0:101 1:0 | A:290587833;C:315368331;G:424558613;T:261915584;N:120876 | 101 | 0 | 290587833 | 315368331 | 424558613 | 261915584 | 120876 | SRX13773731 | SRS11653732 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.89789 | 0.23117 | 0.92843 | 0.77165 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | 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");;