metadata: run_metadata: 3 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and experiment.platform = "DNBSEQ"

3 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and experiment.platform = "DNBSEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
72561	72561	SRR22722190	SRX18683720	SRS16126888	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 R140Q	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:FLT3ITDIDH2R140Q\|BioSampleModel:Model organism or animal	Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R140Q	ITD140Q	ITD140Q	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	ITD172KA_S1_L001_I1_001.fastq.gz ITD172KA_S1_L001_R1_001.fastq.gz ITD172KA_S1_L001_R2_001.fastq.gz	fastq fastq fastq	52149830422.0	410628586.0	ITD172KA S1 L001 I1 001.fastq.gz	0:8 1:28 2:91	A:10282953217;C:8459559201;G:8851285287;T:9772343870;N:1059751	8	28	91	10282953217	8459559201	8851285287	9772343870	1059751	SRX18683720	SRS16126888	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.88465	0.13112	0.81789	0.55842	91	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-14	Adult	Adult	Kidney	Renal System
72562	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
72563	72563	SRR22722192	SRX18683718	SRS16126886	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	Wild type	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:Wild type\|BioSampleModel:Model organism or animal	Single cell RNA seq of Danio rerio: Wild type	Control	Control	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	ControlA_S1_L003_R2_001.fastq.gz ControlA_S1_L003_R1_001.fastq.gz ControlA_S1_L003_I1_001.fastq.gz	fastq fastq fastq	37892727491.0	298367933.0	ControlA S1 L003 I1 001.fastq.gz	0:8 1:28 2:91	A:7386602298;C:6174680460;G:6579652828;T:6955791213;N:54755104	8	28	91	7386602298	6174680460	6579652828	6955791213	54755104	SRX18683718	SRS16126886	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.81686	0.11049	0.84139	0.46084	91	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-14	Adult	Adult	Kidney	Renal System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;