{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kanishk Asthana"],"organism":["Homo sapiens"],"software":["ChronoSeq-Tools"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15894"],"description":["Both Live-cell imaging studies and scRNA-seq studies have shown multiple heterogeneous responses to the same stimulus in the same cells. Therefore as a first application we investigated if ChronoSeq could also reveal the heterogeneity in stimulus response; we applied ChronoSeq to profile inflammatory responses in K562 cells stimulated with TNF-α, to capture the rapid NF-κB signaling cascade. 10 minute interval between samples including a 1 minute sampling duration."],"repository":["biostudies-arrayexpress"],"sample_protocol":["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.","Sequencing - Illumina NovaSeq X 10B on one lane in PE100 configuration with Custom Read 1 primer","Sample Collection - Automated cell sampling using ChronoSeq device. Each cell sample is injected with a unique injection of Time-Tagged ChronoSeq beads."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - hg38 alignment. Data processed using ChronoSeq-Tools pipeline.","Data Transformation - UMIs and gene information were used to generate unique transcripts captured and remove PCR duplicates using Drop-seq tools."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X","ChronoSeq"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Kanishk Asthana"],"additional_accession":[]},"is_claimable":false,"name":"K562 cells treated with 10ng/ml TNFα, profiled with ChronoSeq for 12 samples barcoded with unique Time-Tags","description":"Both Live-cell imaging studies and scRNA-seq studies have shown multiple heterogeneous responses to the same stimulus in the same cells. Therefore as a first application we investigated if ChronoSeq could also reveal the heterogeneity in stimulus response; we applied ChronoSeq to profile inflammatory responses in K562 cells stimulated with TNF-α, to capture the rapid NF-κB signaling cascade. 10 minute interval between samples including a 1 minute sampling duration.","dates":{"release":"2025-11-01T00:00:00Z","modification":"2026-05-26T13:06:43.947Z","creation":"2025-10-29T06:15:13.916Z"},"accession":"E-MTAB-15894","cross_references":{"ENA":["ERP183239"],"EFO":["EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}