{"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-15947"],"description":["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. In addition Puromycin was added at a does of 5μg/ml for blocking translation. The purpose of this experiment was to measure TNF-α stimulation transcriptional program without translational feedback."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.","Growth Protocol - K562 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.html","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.html","Sequencing - Illumina NovaSeq X 10B on one lane in PE100 configuration with Custom Read 1 primer","Sample Treatment - 10ng/ml TNF-α + 5μg/ml Puromycin were added to stimulate the cells and block translation respectively. Both were added together 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.html"],"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. https://github.com/kanishkasthana/ChronoSeq-Tools","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"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Kanishk Asthana"],"additional_accession":[]},"is_claimable":false,"name":"K562 stimulated with TNFα with translation blocking using Puromycin. 12 samples were taken with ChronoSeq and barcodes with unique time-tags","description":"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. In addition Puromycin was added at a does of 5μg/ml for blocking translation. The purpose of this experiment was to measure TNF-α stimulation transcriptional program without translational feedback.","dates":{"release":"2025-11-01T00:00:00Z","modification":"2026-05-26T12:05:31.759Z","creation":"2025-10-31T21:14:10.464Z"},"accession":"E-MTAB-15947","cross_references":{"ENA":["ERP183478"],"Biostudies":["E-MTAB-15927","E-MTAB-15928","E-MTAB-15894"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}