run_metadata: 72562

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
72562	SRR22722191	SRX18683719	SRS16126887	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening					Transgenic FLT3 ITD IDH2 R172K		strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Transgenic Runx1:FLT3ITDIDH2R172K\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R172K	ITD172K	ITD172K	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400		SRP412911		loader:fastq load.py	ITD140QA_S1_L004_I1_001.fastq.gz ITD140QA_S1_L004_R1_001.fastq.gz ITD140QA_S1_L004_R2_001.fastq.gz	fastq fastq fastq	28595025233.0	225157679.0	ITD140QA S1 L004 I1 001.fastq.gz	0:8 1:28 2:91	A:5628987577;C:4565848641;G:4959209904;T:5302394659;N:32908008	8	28	91		5628987577	4565848641	4959209904	5302394659	32908008	SRX18683719	SRS16126887	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.81404		0.11315		0.83327		0.56222		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x		China	2022-12-13	Adult	Adult	Kidney	Renal System