run_metadata: 65589
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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| 65589 | SRR15390211 | SRX11692441 | SRS9724035 | SRP331755 | PRJNA753151 | scRNA seq of fin and body zebrafish melanocytes | GSE181748 | Transcriptome Analysis | Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together taking note of their sample origin. | pubmed:35355015 | XFN | GSM5510267 | source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP | XFN | Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output | Zebrafish fins | Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics | model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP | GSM5510267 | GSM5510267: XFN; Danio rerio; RNA Seq | GSM5510267 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics | GEO Accession:GSM5510267 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP331755 | 2385_XFN_IGO_11718_4_S4_L001_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L001_R2_001.fastq.gz | fastq fastq | 20452607604.0 | 174808612.0 | GSM5510267 r1 | 0:29 1:88 | A:5729911089;C:4526353776;G:4631244451;T:5564405432;N:692856 | 29 | 88 | 5729911089 | 4526353776 | 4631244451 | 5564405432 | 692856 | SRX11692441 | SRS9724035 | SRA1274997 | GEO | White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center | 2 | 0.00608 | 0.85139 | 0.00196 | 0.14282 | 0.99093 | 0.78543 | 0.42676 | 0.53168 | 29 | 88 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-09 | Undetermined | Adult | Fin | Surface Structure |