biostudies-arrayexpressYan YanHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16398We describe ‘nanomaterial-biological hybrid complexes’ composed partly of an engineered nanoparticle core and formed partly by active processes within cells. Thus magnetic nanoparticles are internalized by cells, undergo active biomolecular deposition to form a new overlaid cell-derived corona layer before being re-exported. We have characterised the exported nanostructures by RNA-seq and proteomics analysis.biostudies-arrayexpressSample Collection - HEK293 cells were seeded into T175 flask and cultured for 24 h. The culture medium was then removed, the cells were washed twice with pre-warmed PBS, and pre-warmed serum-free medium was added before incubating for a further 24 h. The conditioned serum-free medium was collected and centrifuged at 2,000 × g for 30 mins at 4 ℃ to remove cells, followed by 16,000 × g for 20 mins at 4 ℃ to remove cell debris. The resulting supernatant was ultracentrifuged at 160,000 × g for 1.5 h at 4 ℃. The pellet was resuspended in PBS and ultracentrifuged again at 160,000 × g for 2 h at 4 ℃. The final pellet was used for proteomics analysis.Library Construction - We used Invitrogen™ Collibri™ Stranded RNA Library Prep Kit for Illumina sequencing.Sample Treatment - The cells were treated with nanoparticles for 10 min pulse followed by 4 hour chase. The conditioned media were collected.Nucleic Acid Extraction - Samples were initially lysed by adding 700 µL QIAzol Lysis Reagent (QIAGEN, Cat. No. 79306), followed by vortexing for 60 sec and incubation at RT (15–25 °C) for 5 min. Subsequently, 140 µL chloroform was added, and samples were shaken vigorously for 15 s. Phase separation was achieved by centrifugation at 14,000 × g for 5 min at RT using QIAGEN MaXtract High Density Tubes. The aqueous phase containing total RNA was collected, and the protocol described in Appendix A of the miRNeasy Micro Kit manual was followed to selectively recover large RNA species (>200 nucleotides) depleted from small RNAs including miRNAs.Sample Collection - A549 cells were washed with PBS and trypsinzed and centrifuged to collect the cell pellets.Growth Protocol - A549 cells were cultured in normal growth media.Library Construction - MGIEasy RNA Library Prep SetSample Treatment - Complete growth media were removed. HEK293 cells were treated with serum-free media for 24hSequencing - single end 50 bp on MGISEQ-2000 platform performed at BGI.Nucleic Acid Extraction - We used QIAGEN miRNeasy Micro Kit (Cat. No. 217084) to extract RNA.Sample Collection - Cells were trypsinzed and collected in a fresh tube. The cells were pelleted by 1000 g for 5 min at 37C. The cell pellets were washed in PBS and re-pelleted.Sample Collection - Cells were exposed to nanoparticle suspension for 10 min (pulse). The suspension was removed. Cells then were incubated complete medium containing FBS for 4 h (chase). After the chase, the supernatants were collected and clarified to remove cell debris. The exported particle complexes were pelleted by centrifugation at 12,000 x g for 40 min at 4 °C.Sequencing - paired-end 100 bp sequencing on the NovaSeq 6000 platform performed the NU-OMICS DNA Sequencing Research Facility, Northumbria University.Growth Protocol - HEK293 cells are cultured in complete growth mediaSample Collection - The supernatant were ultracentrifuged at 160,000 g for 1.5hSequencing - pair end 150 bp on MGISEQ-2000 platform performed at BGI.Sample Treatment - A549 cells were untreated.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSequence Alignment - HISAT2Data Transformation - FeatureCountsMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMGISEQ-2000RSIllumina NovaSeq 6000RNA-seq of total RNAHomo sapiensYan YanfalseBiomolecular Condensate Coronas from Nanoparticle Intracellular Processing Are Transferred Between Cells Allowing Cytosolic and Nuclear AccessWe describe ‘nanomaterial-biological hybrid complexes’ composed partly of an engineered nanoparticle core and formed partly by active processes within cells. Thus magnetic nanoparticles are internalized by cells, undergo active biomolecular deposition to form a new overlaid cell-derived corona layer before being re-exported. We have characterised the exported nanostructures by RNA-seq and proteomics analysis.2026-04-16T00:00:00Z2026-04-17T01:02:05.511Z2025-12-18T00:52:28.095ZE-MTAB-16398ERP186723EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969