run_metadata: 28615

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
28615	SRR26471894	SRX22175827	SRS19233329	SRP467949	PRJNA1031141	Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]	GSE246037	Transcriptome Analysis	Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.	parent bioproject:PRJNA814534	pubmed:38280871		cebp1 wt eos 2	GSM7854236		source name:eosinophils\|strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP\|geo loc name:missing\|collection date:missing	cebp1 wt eos 2	Post quality control the fastq files were mapped to the zebrafish genome with the "STAR" package. Mapped reads were annotated with the "FeatureCounts" package. Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2". The gene expression heatmaps were generated by "pheatmap" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample	eosinophils		Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		strain:AB strain\|tissue:whole larvae\|genotype:wild type\|transgene:Tgeslec:eGFP	GSM7854236	GSM7854236: cebp1 wt eos 2; Danio rerio; RNA Seq	GSM7854236 r1	GSM7854236	1	Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP467949		loader:fastq load.py	W2_1.fq.gz W2_2.fq.gz	fastq fastq	6478425300.0	21594751.0	GSM7854236 r1	0:150 1:150	A:2031706672;C:1135087913;G:1324534931;T:1987064653;N:31131	150	150			2031706672	1135087913	1324534931	1987064653	31131	SRX22175827	SRS19233329	SRA1737851	South China University of Technology	South China University of Technology	2	0.74912	0.74531	0.50454	0.49737	0.79255	0.78539	0.63484	0.64052	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only		China	2023-10-23	Larval	Larval	Whole Organism	All anatomical structures