biostudies-arrayexpressAlexandre FavereauxHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15636Collagen tracks deposited by breast cancer cells contain specific miRNAs which reprogram non-invasive cells into highly pro-metastatic ones by inducing a partial epithelial–mesenchymal transition (EMT) associated with an increase in ECM degradation and cell invasiveness.biostudies-arrayexpressNucleic Acid Extraction - RNA was extracted using the Direct-zol RNA microprep kit (Zymo Research) following manufacturer’s instructions, RNA purity was assessed by capillary electrophoresis (LabChip RNA pico sensitivity assay, Perkin Elmer). For MCF-7 cells internalization mRNA-seq RNA extraction was peformed using Nucleospin RNA kit (Macherey Nagel).Sample Collection - For mRNA and microRNA seq of collagen-tracks, we compared a decellularized ECM decorated with collagen-tracks to a control ECM incubated with conditioned media from the same cells. For the track-containing sample, 140,000 MDA-DDR1-GFP cells were seeded on 4 silicone dishes previously coated with 0.5mg/ml type I collagen (Corning, prepared as previously described). The control dish was coated with 0.5mg/ml type I collagen incubated with conditioned media from the same MDA-DDR1-GFP cells. After an overnight incubation, cells were detached using 12 to 16 baths of 20mM EDTA for 5 min at 37°C. The remaining cells were removed by laser microdissection using PALM type 4 microscope (Zeiss). The decellularized ECM were then lysed with 300µl Trizol and kept at -80°C before being used.Sequencing - Sequencing was performed on a NextSeq 2000 system (Illumina) in a 2x100bp mode.Library Construction - Small-RNA-seq libraries were synthesized using NEXTflex Small-RNA Seq kit v3 (Perkin Elmer) following the manufacturer’s instructions. mRNA were reverse transcribed with an oligo-dT primer containing an adapter sequence and double-stranded cDNA was obtained with a template switching oligo (TSO) containing the same adapter sequence as the oligo-dT. After a pre-amplification with 15 cycles of PCR, we used the NEXTflex Rapid XP DNA-seq kit v2 (Perkin Elmer) to synthesize RNA-seq libraries.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesUnknownTranscriptomicsGenomicsProteomicsDirect-zol RNA microprep kit (Zymo Research), LabChip RNA pico sensitivity assay, Perkin Elmer & Nucleospin RNA kit (Macherey Nagel)NEXTflex Small-RNA Seq kit v3 (Perkin Elmer) & NEXTflex Rapid XP DNA-seq kit v2 (Perkin Elmer)NextSeq 2000PALM type 4 microscope (Zeiss)RNA-seq of total RNAHomo sapiensCancer cells transfer invasive properties through microRNAs contained in collagen-tracksLucile Rouyer, Léa Normand, Elodie Richard, Nathalie Allain, Julie Giraud, Sylvaine Di-Tommaso, Cyril Dourthe, Anne-Aurélie Raymond, Jean-William Dupuy, Kevin Moreau, Richard Iggo, Gaetan McGrogan, Nathalie Dugot-Senant, Anthony Bouter, Sisareuth Tan, Alexandre Favereaux, Violaine Moreau, Reini F. Luco, Manon Ros, Frédéric SaltelAlexandre FavereauxfalseRNA-seq of cancer cell collagen tracksCollagen tracks deposited by breast cancer cells contain specific miRNAs which reprogram non-invasive cells into highly pro-metastatic ones by inducing a partial epithelial–mesenchymal transition (EMT) associated with an increase in ECM degradation and cell invasiveness.2025-12-14T00:00:00Z2025-12-14T12:27:32.788Z2025-09-25T20:45:11.932ZE-MTAB-15636ERP180636EFO_0002944EFO_0004170EFO_0009653EFO_0005518EFO_0004184