run_metadata: 45040

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
45040	SRR6494610	SRX3583936	SRS2852962	SRP130950	PRJNA428951	Cell of origin dictates aggression and stem cell activity in acute lymphoblastic leukemia	GSE108855	Transcriptome Analysis	Subclassification of lymphoid neoplasms is often based on the presumed cell of origin based on T and B progenitor gene expression and the effect of cell lineage on influencing functional characteristics such as aggression and self renewal capacity is largely unknown accounted for in part by lack of experimental models to address these questions. Here we have used transgenic zebrafish to create the first models of Myc induced B ALL and mixed phenotypic B/T ALL opening new avenues for studying the these leukemias in the zebrafish. Our work has utilized syngeneic strain zebrafish limiting dilution cell transplantation and the widely reported rag2 Myc transgenic model to provide new understanding of how strain differences can underlie leukemia onset in the zebrafish model. Even more importantly our work now for the first time has allowed assessment of cell lineage on dictating aggression and leukemia stem cell frequency independent of the underlying oncogenic driver. In total our work uncoveres that T ALLs are more aggressive and have higher numbers of leukemia stem cells when compared with B ALL and mixed phenotypic ALL. Furthermore analysis of our biphenotypic B/T ALL suggests that B cell pathways lock cells in less aggressive and lower stem cell fates and are dominant in regulating these processes when T cell pathways are co regulated within ALL cells. Overall design: The goal of our study is to determine the transcriptional profiles of high and low self renewing capacity tumors. 20 samples total: 11 unique samples 9 samples with biological replicates 6 high self renewing tumors >1% cells could initiate leukemia and 5 low self renewing tumors <1% of cells could initiate leukemia.		pubmed:29749398		9.2A	GSM2915052		tissue:Leukemia cells\|replicate number:1\|self renewal capacity:low\|background strain:CG1\|cell type:blood	9.2A	Demultiplexed reads were aligned using STARDobin et al. 2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: count matrix provided as supplementary file	Leukemia cells		Leukemia cell pellets were mixed 350ul of QIAGEN RLT buffer containing 1% 2 mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. RNA samples were prepped and sequenced on the Illumina HiSeq 2000 platform as previously described in Tang et al. PMID 28878000. RNA from bulk tumors were reverse transcribed and sequenced on the Illumina HiSeq 2000 platform.		replicate number:1\|self renewal capacity:low\|background strain:CG1\|cell type:blood	GSM2915052	GSM2915052: 9.2A; Danio rerio; RNA Seq	GSM2915052		1	Leukemia cell pellets were mixed 350ul of QIAGEN RLT buffer containing 1% 2 mercaptoethanol followed by RNA isolation using the RNAeasy Mini kit QIAGEN. RNA samples were prepped and sequenced on the Illumina HiSeq 2000 platform as previously described in Tang et al. PMID 28878000. RNA from bulk tumors were reverse transcribed and sequenced on the Illumina HiSeq 2000 platform.	GEO Accession:GSM2915052	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP130950			9.2A_R1.fastq.gz 9.2A_R2.fastq.gz	fastq fastq	4360921770.0	42754135.0	GSM2915052 r1	0:51 1:51	A:1079666608;C:1084041944;G:1104190687;T:1087055139;N:5967392	51	51			1079666608	1084041944	1104190687	1087055139	5967392	SRX3583936	SRS2852962	SRA649887	GEO	Pathology, Massachusetts General Hospital	2	0.93401	0.93834	0.24172	0.23839	0.79543	0.79853	0.54668	0.56646	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		United States	2018-01-08	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor