{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alexandre Favereaux"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15636"],"description":["Collagen 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Direct-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 2000","PALM type 4 microscope (Zeiss)"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["Cancer cells transfer invasive properties through microRNAs contained in collagen-tracks"],"pubmed_authors":["Lucile 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 Saltel","Alexandre Favereaux"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of cancer cell collagen tracks","description":"Collagen 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.","dates":{"release":"2025-12-14T00:00:00Z","modification":"2025-12-14T12:27:32.788Z","creation":"2025-09-25T20:45:11.932Z"},"accession":"E-MTAB-15636","cross_references":{"ENA":["ERP180636"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0004184"]}}