{"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-15965"],"description":["We checked our ability to uniquely identify each Time-Tag. We did this by mixing beads from odd numbered Time-Tags with human cells and even numbered Time-Tags with mouse cells manually in bulk. These beads were then washed and combined for Reverse Transcription, library preparation and sequencing. Time-Tag resolved cleanly into either human or mouse dominant with 1.6% or less mixed beads detected for each Time-Tag."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.","Sample Collection - Cells were manually mixed directly with the beads. 10μl of Time-Tagged beads at 450 beads/μl suspended in lysis buffer were directly mixed with 8μl of mouse or human cells at 600cells/μl. Odd numbered Time-Tags were mixed with human(K562) cells while even numbered Time-Tags were mixed with mouse(EL4) cells.","Library Construction - Beads are washed once with 6X SSC buffer and then twice with 1.25X RT buffer. Beads were then pooled together for a single RT reaction. very similar to Drop-seq. 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"],"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"],"species":["mixed sample"],"pubmed_authors":["Kanishk Asthana"],"additional_accession":[]},"is_claimable":false,"name":"Bulk K562 and EL4 cells mixed with 12 Time-Tags for verification (QC) for ChronoSeq Beads","description":"We checked our ability to uniquely identify each Time-Tag. We did this by mixing beads from odd numbered Time-Tags with human cells and even numbered Time-Tags with mouse cells manually in bulk. These beads were then washed and combined for Reverse Transcription, library preparation and sequencing. Time-Tag resolved cleanly into either human or mouse dominant with 1.6% or less mixed beads detected for each Time-Tag.","dates":{"release":"2025-11-03T00:00:00Z","modification":"2026-05-26T17:12:38.337Z","creation":"2025-11-03T16:24:21.092Z"},"accession":"E-MTAB-15965","cross_references":{"ENA":["ERP183602"],"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_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}