run_metadata: 26503

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
26503	SRR26031759	SRX21749008	SRS18856548	SRP459729	PRJNA1015262	Rtf1 dependent transcriptional pausing regulates cardiogenesis	PRJNA1015262	Other	During heart development an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis we found that Rtf1 is essential for cardiogenesis and that without xxx activity cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain which confers interaction with the pausing/elongation factor Spt5 was required for Rtf1's ability to support cardiac progenitor formation while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced suggesting a reduction in transcriptional pausing. Intriguingly pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.					RNAseq hand2FACS control 2		strain:TgBAChand2:EGFPpd24\|dev stage:10 12 somite stage\|collection date:2019 12 19\|geo loc name:USA:California Los Angeles\|sex:n/a\|tissue:hand2:GFP positive cells\|BioSampleModel:Model organism or animal									RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos	C2	CTL2	NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina HiSeq 3000		SRP459729			RNAseq_hand2FACS_control_2.fastq	fastq	317458963.0	6417814.0	RNAseq hand2FACS control 2.fastq	0:49.47	A:83925064;C:70621123;G:68872886;T:93923129;N:116761	49				83925064	70621123	68872886	93923129	116761	SRX21749008	SRS18856548	SRA1709841	University of California, Los Angeles\|Molecular, Cell, and Developmental Biology	University of California, Los Angeles	1	0.85587		0.08493		0.75558		0.51678		50		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown		United States	2023-09-11	Segmentation	Embryo	Embryo Imprecise	All anatomical structures