run_metadata: 76585

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
76585	SRR25181149	SRX20928872	SRS18204809	SRP447851	PRJNA991987	RNA seq for gata1+ cells in add1 mutant zebrafish embryos and siblings at 22 hpf	GSE236659	Transcriptome Analysis	Adducin 1 Add1 functions primarily as a membrane cytoskeletal protein whereas Add1 contains a bipartite nuclear localization signal implying its special nuclear function. However the nuclear functional roles of Add1 apart from maintaining cytoskeletal stability remain unknown. Here we created add1 deficient zebrafish using Tol2 transposon mediated gene trapping and evaluated how add1 deficiency affected early hematopoiesis development. When add1 is lacking in zebrafish both the primitive erythropoiesis and definitive hematopoiesis are compromised and the primitive erythroblast cells are unable to develop into healthy erythrocytes. More significantly the RNA sequencing results demonstrated that the p53 pathway is activated in the add1 depletion erythroblast cells causing the erythroblasts to undergo apoptosis at the 14 somites stage and 24 hpf. Additionally the anemic phenotype and apoptosis in add1 deficient embryos can be partially rescued by p53 insufficiency. Taken together our findings show that add1 is critical for zebrafish erythropoiesis partially through the p53 mediated apoptotic pathway which expands the regulatory role of Add1 for nuclear function. Overall design: To better understand the nuclear specific function of add1 we used RNA seq to analyze transcriptome changes in gata1 EGFP positive cells sorted from add1 deficient embryos and siblings at 22 hpf when the differences in the number of erythrocytes were not yet evident in add1 mutant embryos. Comparative gene expression profiling analysis of RNA seq data for erythroblast of add1 mutant and siblings.		pubmed:37636049		WT	GSM7567236		tissue:erythroblast\|cell type:erythroblast\|genotype:wildtype\|geo loc name:missing\|collection date:missing	WT	For gene expression analysis the matched reads were calculated and then normalized to RPKM using RESM software The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio ≥1 and FDR ≤ 0.001. Library construction and sequencing were performed on a BGISEQ 500. Assembly: GRCz10.81 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file include RPKM values for each Sample	erythroblast		Total RNA was isolated using SMART Seq® HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.		cell type:erythroblast\|genotype:wildtype	GSM7567236	GSM7567236: WT; Danio rerio; RNA Seq	GSM7567236 r1	GSM7567236	1	Total RNA was isolated using SMART Seq® HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP447851			WT_1.fq.gz WT_2.fq.gz	fastq fastq	6503251500.0	21677505.0	GSM7567236 r1	0:150 1:150	A:1785076844;C:1448752781;G:1570097457;T:1699269694;N:54724	150	150			1785076844	1448752781	1570097457	1699269694	54724	SRX20928872	SRS18204809			Children's Hospital of Capital Institute of Pediatrics	2	0.94793	0.94488	0.07407	0.07319	0.75493	0.75578	0.45437	0.45369	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2023-07-06	Undetermined	Embryo	Blood	Hematopoietic System