run_metadata: 70452

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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
70452	SRR19859705	SRX15903236	SRS13591716	SRP383719	PRJNA853194	The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Huët anomaly and promoting sAML transformation	GSE206979	Transcriptome Analysis	Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils and progressed to MDS/AML with a high ratio. Interestingly a group of poorly differentiated Pelger Huët like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype c mybhyper pu.1G242D/G242D c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.		pubmed:40020188		km wildtype replicate 1	GSM6267520		source name:kidney marrow\|development stage:1 year old\|tissue:kidney marrow\|cell type:blood cells\|genotype:wt	km wildtype replicate 1	10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets using the PC distance to find each cell’s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs ≥40000 or mitochondrial gene percent ≥15% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset we employed a global scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression multiplies this by a scale factor 10 000 by default and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files matrix files	kidney marrow		Kidney marrow were isolated from 1 year old fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90% the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Briefly blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM primers containing an Illumina® R1 sequence a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		development stage:1 year old\|tissue:kidney marrow\|cell type:blood cells\|genotype:wt	GSM6267520	GSM6267520: km wildtype replicate 1; Danio rerio; RNA Seq	GSM6267520 r1	GSM6267520	1	Kidney marrow were isolated from 1 year old fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90% the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM primers containing an Illumina® R1 sequence a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP383719			wildtype_S1_L001_R2_001.fastq.gz wildtype_S1_L001_R1_001.fastq.gz	fastq fastq	27770111700.0	92567039.0	GSM6267520 r1	0:150 1:150	A:10654881712;C:5315111692;G:4977483030;T:6822156857;N:478409	150	150			10654881712	5315111692	4977483030	6822156857	478409	SRX15903236	SRS13591716	SRA1444282	Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology	Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology	2	0.0	0.90999	0.0	0.06416	1.0	0.83909		0.46343	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2022-06-27	Adult	Adult	Kidney	Renal System