run_metadata: 28865

This data as json

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
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