run_metadata: 68917
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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| 68917 | SRR18220755 | SRX14367193 | SRS12180288 | SRP362487 | PRJNA812890 | MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells | GSE197927 | Transcriptome Analysis | Uveal melanoma UM is the most common primary malignancy of the eye in adults but lacks any FDA approved therapy for the deadly metastatic disease. Thus there is great need to dissect the driving mechanisms for UM and develop strategies to evaluate potential therapeutics. Using a zebrafish model we previously identified MITF the master melanocyte transcription factor as a tumor suppressor in GNAQQ209L driven UM. Here we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state as well as expression of GNAQQ209L YAPS127A;S381A or BRAFV600E oncogenes impacts melanocyte lineage cells before they acquire the transformed state. Specifically examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall this study establishes that a neural crest signature correlates with poor UM survival and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF GNAQ and YAP transgenes. | pubmed:35869673 | YAP.Mm rep 4 | GSM5934073 | tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+ half tp53 +/+ | YAP.Mm rep 4 | HiSeq 2000 using v3 chemistry. Software: Control v2.2.58 RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson Love and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset | cells isolated from 5 dpf larvae that express a mitfa:GFP reporter | Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine. | RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads. | genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+ half tp53 +/+ | GSM5934073 | GSM5934073: YAP.Mm rep 4; Danio rerio; RNA Seq | GSM5934073 r1 | GSM5934073 | 1 | RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP362487 | d3657.fq.gz | fastq | 505578840.0 | 12639471.0 | GSM5934073 r1 | 0:40 | A:151358215;C:100212599;G:101677867;T:152291228;N:38931 | 40 | 151358215 | 100212599 | 101677867 | 152291228 | 38931 | SRX14367193 | SRS12180288 | SRA1380881 | Koch Institute | Koch Institute | 1 | 0.88348 | 0.15567 | 0.73016 | 0.54726 | 40 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Unknown | 2022-03-04 | Larval | Larval | Undetermined | Undetermined |