{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kanishk Asthana"],"organism":["mixed sample"],"software":["ChronoSeq-Tools"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15964"],"description":["Automated sampling within the ChronoSeq device showed similarly precise tagging: when human, mouse, and mixed reservoirs were processed in sequence, each cell population was exclusively labeled with its designated barcode. Goal of this experiment was to show accurate Time-Tagging of each sample with the ChronoSeq device."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.","Library Construction - ChronoSeq library preparation protocol is very similar to Drop-seq. Beads from all time-tags are pooled together for Reverse Transcription followed by PCR amplification. https://kanishkasthana.github.io/ChronoSeq/protocol_library_preparation_for_dropseq_chronoseq_beads.html","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.html","Sequencing - Illumina NovaSeq X 10B on one lane in PE150 configuration with Custom Read 1 primer. 10% PhiX spike in. Mix primers with Illumina Primers","Sample Collection - K562+EL4 (Time Tag 10), K562(Time Tag 11), EL4 (Time Tag 12). 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"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - mm10-hg19 Drop-seq mixed reference used for 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":["mixed sample"],"pubmed_authors":["Kanishk Asthana"],"additional_accession":[]},"is_claimable":false,"name":"K562+EL4 (Time Tag 10), K562(Time Tag 11), EL4 (Time Tag 12) (QC) 215 cells/ μl 3 Time-Tags. ChronoSeq No Stimulus. Only Checking Time-Tags with a Sampling Interval of 7minutes","description":"Automated sampling within the ChronoSeq device showed similarly precise tagging: when human, mouse, and mixed reservoirs were processed in sequence, each cell population was exclusively labeled with its designated barcode. Goal of this experiment was to show accurate Time-Tagging of each sample with the ChronoSeq device.","dates":{"release":"2025-11-03T00:00:00Z","modification":"2026-05-26T22:02:54.357Z","creation":"2025-11-03T16:20:13.313Z"},"accession":"E-MTAB-15964","cross_references":{"ENA":["ERP183599"],"Biostudies":["E-MTAB-15927","E-MTAB-15928","E-MTAB-15956","E-MTAB-15955","E-MTAB-15947","E-MTAB-15946","E-MTAB-15894"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}