{"database": "metadata", "table": "run_metadata", "rows": [[76525, "SRR24999169", "SRX20755038", "SRS18043615", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex  to regulate gfi1aa expression   during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia  neutrophilia  and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor  whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically  Znf687 functions as a negative regulator of gfi1aa  a pivotal modulator in terminal granulopoiesis  to regulate neutrophil maturation. Moreover  we found BRD4  an important epigenetic regulator  interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator  Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall  our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis  but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 1", "GSM7506190", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 1", "We filter the low quality reads More than 20% of the bases qualities are lower than 10  reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6   and then calculate gene expression level with RSEMv1.2.12. Then  we calculate pearson correlation between all samples using cor  perform hierarchical clustering between all samples using hclust  perform PCA analysis with all samples using princomp  and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506190", "GSM7506190: Tgmpx:eGFP 1; Danio rerio; RNA Seq", "GSM7506190 r1", "GSM7506190", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen  Manchester  UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co.  Ltd.  Nanjing  China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mpx-11-10_combined_R1.fastq.gz", "fastq fastq", 7364874300.0, 24549581.0, "GSM7506190 r1", "0:150 1:150", "A:1988715009;C:1657810285;G:1778472191;T:1939822538;N:54277", 150, 150, null, null, 1988715009, 1657810285, 1778472191, 1939822538, 54277, "SRX20755038", "SRS18043615", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94842, 0.94741, 0.10807, 0.10703, 0.69451, 0.69552, 0.4957, 0.49509, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Hatching", "Embryo", "Blood", "Hematopoietic System"]], "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": ["76525"], "units": {}, "query_ms": 9.652453009039164}