run_metadata: 41084
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41084 | SRR3666784 | SRX1845189 | SRS1504028 | SRP076552 | PRJNA325656 | Differential gene expression of zebrafish melanocytes and melanomas [RNA seq] | GSE83343 | Transcriptome Analysis | We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types | parent bioproject:PRJNA325808 | pubmed:29202482 | ZF melanoma rep4 | GSM2199909 | tissue:melanoma|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4|age:adult|cell type:melanoma | ZF melanoma rep4 | Star v2.3 was used to align the reads htseq count was used to count mappped reads DESeq2 was used to perform differential gene expression analysis Genome build: Zebrafish Zv9 Supplementary files format and content: tab delimited txt file includes FPKM values for all samples | melanoma | RNA was harvested from cells using Trizol reagent. Illumina TruSeq | Unpigmented EGFP positive melanocytes and melanoma cells were isolated by FACS | strain:Tgmitfa:BRAFV600E;p53zdf1;Tgmitfa:EGFP;albb4|age:adult|cell type:melanoma | GSM2199909 | GSM2199909: ZF melanoma rep4; Danio rerio; RNA Seq | GSM2199909 | 1 | RNA was harvested from cells using Trizol reagent. Illumina TruSeq | GEO Accession:GSM2199909 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP076552 | Melanoma_4_R1.fastq.gz Melanoma_4_R2.fastq.gz | fastq fastq | 5824407060.0 | 57102030.0 | GSM2199909 r1 | 0:51 1:51 | A:1623471404;C:1272539670;G:1281078941;T:1643101126;N:4215919 | 51 | 51 | 1623471404 | 1272539670 | 1281078941 | 1643101126 | 4215919 | SRX1845189 | SRS1504028 | SRA433946 | GEO | PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts | 2 | 0.9269 | 0.87875 | 0.16101 | 0.15437 | 0.75601 | 0.76479 | 0.52959 | 0.49449 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-06-14 | Adult | Adult | Cancer or Tumor | Cancer or Tumor |