run_metadata: 30014

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
30014	SRR28164888	SRX23795140	SRS20618184	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 12 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 12 hpf CMO		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf CMO\|dev stage:12 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 12 hpf CMO	C 1	C 1	10x Genomics multiplexing CMO			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP485064			12h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 12h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	23801259900.0	79337533.0	12h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:5110000752;C:5818733743;G:7758205963;T:5113684708;N:634734	150	150			5110000752	5818733743	7758205963	5113684708	634734	SRX23795140	SRS20618184	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2024-02-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures