biostudies-arrayexpressKanishk AsthanaHomo sapiensChronoSeq-Toolshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15927The intent of the experiment was to observe the response of K562 cells when stimulated with LPS. To show that K562 cells cannot respond to LPS either alone or when mixed with cells unresponsive to LPS; we LPS stimulated a 50:50 mixture of K562 and undifferentiated U937 cells which are known to show limited or no response to LPS. Cells were stimulated with 0.5ug/ml of LPS with a sampling interval of 10 minutes.biostudies-arrayexpressNucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.Sample 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 - 0.5ug/ml LPS manually added to Cell Sample Reservoir 5 minutes after first sample/time-tagGrowth Protocol - 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.htmlLibrary 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 - hg38 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 cellsHomo sapiensKanishk Asthanafalse50:50 mixture of U937 and K562 cells treated with 0.5μg/ml of LPS, profiled with ChronoSeq for 12 samples barcoded with unique Time-TagsThe intent of the experiment was to observe the response of K562 cells when stimulated with LPS. To show that K562 cells cannot respond to LPS either alone or when mixed with cells unresponsive to LPS; we LPS stimulated a 50:50 mixture of K562 and undifferentiated U937 cells which are known to show limited or no response to LPS. Cells were stimulated with 0.5ug/ml of LPS with a sampling interval of 10 minutes.2025-11-01T00:00:00Z2026-04-16T20:12:06.767Z2025-10-30T12:50:22.782ZE-MTAB-15927ERP183381E-MTAB-15894EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969