run_metadata: 50856
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 50856 | SRR8312795 | SRX5126176 | SRS4139298 | SRP173302 | PRJNA509471 | The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia. | GSE123665 | Transcriptome Analysis | Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However purifying them from within the bulk tumor has been challenging so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition the side population within the leukemia evolves with serial transplantation increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors | pubmed:30630989 | nonSP 1404 | GSM3509258 | source name:ALL tumor|strain:CG2|tissue:ALL | nonSP 1404 | Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0 edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10. | ALL tumor | None | Tumors were removed sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | None | strain:CG2|tissue:ALL | GSM3509258 | GSM3509258: nonSP 1404; Danio rerio; RNA Seq | GSM3509258 | 1 | Tumors were removed sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM3509258 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP173302 | 2069543600.0 | 41390872.0 | GSM3509258 r1 | 0:50 1:0 | A:459382162;C:532071054;G:508544948;T:569228380;N:317056 | 50 | 0 | 459382162 | 532071054 | 508544948 | 569228380 | 317056 | SRX5126176 | SRS4139298 | SRA822847 | GEO | Bioinformatics Core, Biological Sciences Division, The University of Chicago | 1 | 0.96095 | 0.06905 | 0.83412 | 0.4818 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2018-12-11 | Undetermined | Undetermined | Cancer or Tumor | Cancer or Tumor |