run_metadata: 67040
This data as json
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| 67040 | SRR17007610 | SRX13197806 | SRS11124866 | SRP347244 | PRJNA782626 | Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content | GSE189352 | Transcriptome Analysis | Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples. | pubmed:35628321 | VA 24 S14: Melanoma3 | GSM5699729 | tissue:Melanoma3|cell type:Melanocytes|strain:kita:RAS | VA 24 S14: Melanoma3 | Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample | Melanoma3 | RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. | Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid | cell type:Melanocytes|strain:kita:RAS | GSM5699729 | GSM5699729: VA 24 S14: Melanoma3; Danio rerio; ncRNA Seq | GSM5699729 r1 | GSM5699729 | 1 | RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP347244 | loader:fastq load.py | VA_24_S14.fastq | fastq | 1029043954.0 | 10188554.0 | GSM5699729 r1 | 0:101 | A:385266918;C:235984418;G:223100119;T:184638731;N:53768 | 101 | 385266918 | 235984418 | 223100119 | 184638731 | 53768 | SRX13197806 | SRS11124866 | SRA1429699 | Experimental Cancer Biology, CIBIO, University of Trento | Experimental Cancer Biology, CIBIO, University of Trento | 1 | 0.31444 | 0.04431 | 0.97477 | 0.79077 | 101 | B | usable mapping rate | illumina | hiseq_era | full_length | size_fractionation | smarter | bulk | unknown | unknown | Italy | 2021-11-22 | Adult | Adult | Cancer or Tumor | Cancer or Tumor |