biostudies-arrayexpressKanishk Asthanamixed sampleChronoSeq-Toolshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15965We checked our ability to uniquely identify each Time-Tag. We did this by mixing beads from odd numbered Time-Tags with human cells and even numbered Time-Tags with mouse cells manually in bulk. These beads were then washed and combined for Reverse Transcription, library preparation and sequencing. Time-Tag resolved cleanly into either human or mouse dominant with 1.6% or less mixed beads detected for each Time-Tag.biostudies-arrayexpressNucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.Sample Collection - Cells were manually mixed directly with the beads. 10μl of Time-Tagged beads at 450 beads/μl suspended in lysis buffer were directly mixed with 8μl of mouse or human cells at 600cells/μl. Odd numbered Time-Tags were mixed with human(K562) cells while even numbered Time-Tags were mixed with mouse(EL4) cells.Library Construction - Beads are washed once with 6X SSC buffer and then twice with 1.25X RT buffer. Beads were then pooled together for a single RT reaction. very similar to Drop-seq. https://kanishkasthana.github.io/ChronoSeq/protocol_library_preparation_for_dropseq_chronoseq_beads.htmlGrowth Protocol - K562 and EL4 cells grown in suspension in DMEM with 10% FBS and 1%PEN-STREP at 5%CO2 and 37C. https://kanishkasthana.github.io/ChronoSeq/protocol_for_preparing_cells_AdditionalFiltration.htmlSequencing - Illumina NovaSeq X 10B on one lane in PE150 configuration with Custom Read 1 primer. 10% PhiX spike in. Mix primers with Illumina PrimersOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - mm10-hg19 Drop-seq mixed reference used for alignment. Data processed using ChronoSeq-Tools pipeline. https://github.com/kanishkasthana/ChronoSeq-ToolsData Transformation - UMIs and gene information were used to generate unique transcripts captured and remove PCR duplicates using Drop-seq tools.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAmixed sampleKanishk AsthanafalseBulk K562 and EL4 cells mixed with 12 Time-Tags for verification (QC) for ChronoSeq BeadsWe checked our ability to uniquely identify each Time-Tag. We did this by mixing beads from odd numbered Time-Tags with human cells and even numbered Time-Tags with mouse cells manually in bulk. These beads were then washed and combined for Reverse Transcription, library preparation and sequencing. Time-Tag resolved cleanly into either human or mouse dominant with 1.6% or less mixed beads detected for each Time-Tag.2025-11-03T00:00:00Z2026-05-26T17:12:38.337Z2025-11-03T16:24:21.092ZE-MTAB-15965ERP183602E-MTAB-15927E-MTAB-15928E-MTAB-15956E-MTAB-15955E-MTAB-15947E-MTAB-15946E-MTAB-15894EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184