run_metadata: 76523

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
76523	SRR24999167	SRX20755040	SRS18043617	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.		pubmed:38326409		Tgmpx:eGFP larvae injected with znf687a MO 1	GSM7506192		source name:hematopoietic\|tissue:hematopoietic\|cell line:mpx+\|cell type:neutrophil\|genotype:znf687a knowdown\|treatment:znf687a MO\|geo loc name:missing\|collection date:missing	Tgmpx:eGFP larvae injected with znf687a MO 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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.	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:znf687a knowdown\|treatment:znf687a MO	GSM7506192	GSM7506192: Tgmpx:eGFP larvae injected with znf687a MO 1; Danio rerio; RNA Seq	GSM7506192 r1	GSM7506192	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP445421			R21136162-qtsw-z003-mo-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mo-11-10_combined_R1.fastq.gz	fastq fastq	5474240400.0	18247468.0	GSM7506192 r1	0:150 1:150	A:1344187663;C:1136523926;G:1697034586;T:1296453731;N:40494	150	150			1344187663	1136523926	1697034586	1296453731	40494	SRX20755040	SRS18043617	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	0.85041	0.8461	0.08081	0.07986	0.74328	0.746	0.48356	0.47751	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk		China	2023-06-22	Multi-stage	Multi-stage	Blood	Hematopoietic System