biostudies-arrayexpressKanishk AsthanaHomo sapiensChronoSeq-Toolshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15928The purpose of this experiment was to observe secondary signaling response of THP-1 to K562 cells observed in real time with ChronoSeq. Cells were sampled every 15 minutes. LPS was added 5 minutes after the first sample. Watchmaker RNAase inhibitor of 800U/μl was added to all Time-Tagged beads for a final concentration of 3U/μl, because of high RNAase activity in THP-1 supernatants.biostudies-arrayexpressNucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.Sample Treatment - 1ug/ml LPS manually added to Cell Sample Reservoir 5 minutes after first sample/time-tagGrowth Protocol - For K562Cells grown in suspension in DMEM with 10% FBS and 1%PEN-STREP at 5%CO2 and 37C. THP-1 cells were first grown in suspension same as K562 and then treated with 100nM PMA to induce differenciation for 48 hours. This was followed by a 72 hour rest period before harvesting with 10mM EDTA in DPBS. 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 primerLibrary 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 differentiated THP-1 macrophages and K562 cells treated with 1μg/ml of LPS, profiled with ChronoSeq for 12 samples barcoded with unique Time-TagsThe purpose of this experiment was to observe secondary signaling response of THP-1 to K562 cells observed in real time with ChronoSeq. Cells were sampled every 15 minutes. LPS was added 5 minutes after the first sample. Watchmaker RNAase inhibitor of 800U/μl was added to all Time-Tagged beads for a final concentration of 3U/μl, because of high RNAase activity in THP-1 supernatants.2025-11-01T00:00:00Z2026-05-26T10:32:13.909Z2025-10-30T12:56:31.101ZE-MTAB-15928ERP183383E-MTAB-15894EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969