{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["René Wardenaar"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14473"],"description":["To better understand the mechanism underlying the invasion and migration phenotype instigated by EFEMP1 EVs (extracellular vesicles), we performed RNA sequencing analysis on BT549 cells treated with control and EFEMP1KD EVs."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was conducted on the Illumina NextSeq 2000 system using a P2 100 cycle kit. Run specifications included a read 1 of 113 bp, read 2 of 7 bp, index 1 of 9 bp, index 2 of 9 bp, loaded molarity of 750 pM, and a phiX percentage of 5%.","Sample Collection - BT549 WT cells were seeded as recipient cells. EVs (extracellular vesicles) from scramble control EVs and EFEMP1 kd EVs were used to treat the WT cells for 24 hours. And then the cell pellets were collected.","Nucleic Acid Extraction - RNA was extracted using the RNA plus isolation kit (Qiagen, 74136) following the protocols.","Library Construction - RNA quality control (QC) involved concentration assessment using Nanodrop and quality and RIN value measurement via HSRNA screentape assay or RNA screentape assay on the Agilent 4200 Tapestation system. Library preparation employed the Smart-3seq method on an Agilent Bravo Automated Liquid Handling Platform, using 100 ng input per sample. For lower-concentration samples, a pre-bead clean-up (poly A RNA capturing) with SPRI beads was performed. Indexes utilized were NEBNext Multiplex oligos for Illumina (E6440L) with 12 PCR cycles. Bead clean-up was done twice at a 0.8x ratio. Post-library preparation QC included concentration measurement using Qubit 1X dsDNA HS Assay Kit and BioTek Synergy H1 Multimode Reader, with molarity assessment via HSD5000 or D5000 screentape assay on the Agilent 4200 Tapestation system. Libraries were diluted to 4 nM and pooled. Superpool concentration and molarity verification employed the Qubit 1X dsDNA HS Assay Kit, Qubit 4 Fluorometer, and HSD5000 screentape assay."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Chromosomal instability promotes cell migration and invasion via EFEMP1 in extracellular vesicles"],"pubmed_authors":["Zheng et al.","René Wardenaar"],"additional_accession":[]},"is_claimable":false,"name":"Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion in extracellular vesicles","description":"To better understand the mechanism underlying the invasion and migration phenotype instigated by EFEMP1 EVs (extracellular vesicles), we performed RNA sequencing analysis on BT549 cells treated with control and EFEMP1KD EVs.","dates":{"release":"2025-09-13T00:00:00Z","modification":"2025-09-13T01:02:42.248Z","creation":"2024-09-23T21:56:03.081Z"},"accession":"E-MTAB-14473","cross_references":{"ENA":["ERP164448"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}