{"database": "metadata", "table": "run_metadata", "rows": [[28617, "SRR26471896", "SRX22175825", "SRS19233327", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df 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 Cebp\u00df 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", null, "cebp1 mut eos 2", "GSM7854234", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebp1 mut 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", null, "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.", null, "strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP", "GSM7854234", "GSM7854234: cebp1 mut eos 2; Danio rerio; RNA Seq", "GSM7854234 r1", "GSM7854234", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "M2_2.fq.gz M2_1.fq.gz", "fastq fastq", 6104680800.0, 20348936.0, "GSM7854234 r1", "0:150 1:150", "A:1804058925;C:1198439018;G:1326225576;T:1775930488;N:26793", 150, 150, null, null, 1804058925, 1198439018, 1326225576, 1775930488, 26793, "SRX22175825", "SRS19233327", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.8123, 0.81465, 0.42735, 0.42341, 0.78171, 0.77567, 0.46764, 0.65485, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["28617"], "units": {}, "query_ms": 12.933831999362155}