run_metadata: 35912

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
35912	SRR33227834	SRX28474908	SRS24794874	SRP580008	PRJNA1253320	Prpf4 Sequentially Regulates the Expansion and Maturation of Erythrocyte through Distinct Mechanisms	PRJNA1253320	Other	The proliferation of early erythrocyte and the subsequent erythrocyte maturation are critical events during erythropoiesis how these two independent but interconnected processes are efficiently orchestrated during erythropoiesis was largely unknown. Prpf4 expression is enriched from Pre Colony Forming Unit Erythroid PreCFU E to Nucleated Erythrocytes especially in the CFU E cells implying Prpf4 plays a critical role in erythropoiesis. Here we demonstrate that prpf4 sequentially regulates erythrocyte proliferation and maturation during zebrafish definitive hematopoiesis. The data show that prpf4 mutation results in severe defects in erythropoiesis characterized by a substantial reduction in erythroid cell numbers and impaired erythrocyte maturation. Further analysis indicates that prpf4 mutation leads to cell cycle arrest of erythrocytes at the S and G2/M phases as well as a significant increase in erythrocyte apoptosis. Mechanistically prpf4 mutation leads to DNA damage and the subsequent activation of DNA damage response triggering the ATM/CHK2 p53 signaling pathway. This process inhibits the proliferation of early erythrocyte and induces erythrocyte apoptosis. On the other hand the data reveal that prpf4 mutation causes significant defect in skipped exon during pre mRNA splicing accompanying severe splicing defect in slc25a39 pre mRNA. This results in a significant downregulation of slc25a39 mRNA ultimately impairing erythrocyte maturation in late erythropoiesis. In conclusion we identify that prpf4 sequentially regulates early erythrocyte proliferation and the sequential erythrocyte maturation the dual function of prpf4 partially explaining how early erythrocyte proliferation and late erythrocyte maturation are efficiently coordinated during erythropoiesis.				RNA seq of WT zebrafish at 48 hpf	Prpf4 WT rep2		strain:AB\|isolate:embryo pool 5\|breed:wild type\|ecotype:laboratory strain\|age:48 hpf\|dev stage:embryo\|collection date:2023 11\|geo loc name:China: Sichuan Chengdu\|sex:not applicable\|tissue:erythrocytes\|BioSampleModel:Model organism or animal									RNA seq of wild type zebrafish at 48 hpf	lib Prpf4 WT rep2	lib Prpf4 WT rep2	Same as above			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus		SRP580008			Prpf4_WT_rep2_R1_001.fastq.gz Prpf4_WT_rep2_R2_001.fastq.gz	fastq fastq	6071219400.0	20237398.0	Prpf4 WT rep2 R1 001.fastq.gz	0:150 1:150	A:1485039562;C:1529219051;G:1507447307;T:1549077264;N:436216	150	150			1485039562	1529219051	1507447307	1549077264	436216	SRX28474908	SRS24794874	SRA2115340	Chengdu medical college\|School of Basic Medical Sciences	Chengdu medical college												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2025-04-20	Hatching	Embryo	Embryo Imprecise	All anatomical structures