biostudies-arrayexpressKanishk Asthanamixed sampleChronoSeq-Toolshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15956This was a QC experiment to estimate the doublet rate with a species mixing experiment (Human+Mouse) at this cell concentration when used with the ChronoSeq device.biostudies-arrayexpressNucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.Growth 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.htmlSample Collection - Automated cell sampling using ChronoSeq device. Each cell sample is injected with a unique injection of Time-Tagged ChronoSeq beads. https://kanishkasthana.github.io/ChronoSeq/protocol_and_software_for_running_chronoseq_device.htmlSequencing - Illumina NovaSeq X 10B on one lane in PE100 configuration with Custom Read 1 primerSample Treatment - 10ng/ml TNF-α added to stimulate the cells. Added 5 minutes after first sample.Library Construction - ChronoSeq library preparation protocol is very similar to Drop-seq. Beads from all time-tags are pooled together, then split into four equal parts for Reverse Transcription followed by PCR amplification. https://kanishkasthana.github.io/ChronoSeq/protocol_library_preparation_for_dropseq_chronoseq_beads.htmlOrganizationMINSEQE 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 RNA from single cellsmixed sampleKanishk Asthanafalse50:50 K562:EL4 (QC) at 430 cells/ μl with 10ng/ml TNF-α add 5 minutes after first sample and a sampling interval of 10 minutes. A total of three samples taken with ChronoSeq and tagged with three unique time-tagsThis was a QC experiment to estimate the doublet rate with a species mixing experiment (Human+Mouse) at this cell concentration when used with the ChronoSeq device.2025-11-01T00:00:00Z2026-05-26T19:03:45.035Z2025-11-01T17:50:09.626ZE-MTAB-15956ERP183503E-MTAB-15927E-MTAB-15928E-MTAB-15947E-MTAB-15946E-MTAB-15894EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969