run_metadata: 68903
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 |
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| 68903 | SRR18218082 | SRX14364493 | SRS12177788 | SRP362416 | PRJNA812715 | Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia | PRJNA812715 | Other | T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential. | WKM CG1 P2mut 5 | strain:CG1|age:8 month|sex:not collected|tissue:whole kidney marrow|birth date:17 11 2018|death date:17 07 2019|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:WKM CG1 P2mut biological replicate 4|BioSampleModel:Model organism or animal | RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1 | WKM CG1 P2mut 5 | WKM CG1 P2mut 5 | CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000. | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP362416 | FCHT5GHDSXX_L1_HKRDZEBmfpEAAIRAAPEI-P2A2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAIRAAPEI-P2A2_2.fq.gz | fastq fastq | 18218380200.0 | 60727934.0 | FCHT5GHDSXX L1 HKRDZEBmfpEAAIRAAPEI P2A2 1.fq.gz | 0:150 1:150 | A:4769839227;C:4349260666;G:4417289893;T:4681963719;N:26695 | 150 | 150 | 4769839227 | 4349260666 | 4417289893 | 4681963719 | 26695 | SRX14364493 | SRS12177788 | SRA1380603 | Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab | Instituto de Medicina Molecular Joao Lobo Antunes | 2 | 0.94341 | 0.94473 | 0.04954 | 0.04988 | 0.71192 | 0.7121 | 0.52338 | 0.52876 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Portugal | 2022-03-04 | Adult | Adult | Kidney | Renal System |