{"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-15966"],"description":["Time-Tags were mixed 1 through 12. Data was also used for comparison with 10X Genomics 3' Chromium on K562 cells and with Single-Cell RNA-Seq negative control. Cells were not stimulated but maintained inside the ChronoSeq device for sampling. Samples were taken every 10 minutes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Oligo-DT beads were used to capture mRNA from lysed Single-Cells inside droplets.","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","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 - Cells were automatically samples using the ChronoSeq device. 10μl of Time-Tagged beads at 450 beads/μl suspended in lysis buffer were directly mixed with human cells at 600cells/μl. In order 1->12","Growth Protocol - K562 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"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - UMIs and gene information were used to generate unique transcripts captured and remove PCR duplicates using Drop-seq tools.","Sequence Alignment - hg38 reference used for alignment. Data processed using ChronoSeq-Tools pipeline. https://github.com/kanishkasthana/ChronoSeq-Tools"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Kanishk Asthana"],"additional_accession":[]},"is_claimable":false,"name":"Bulk K562 cells negative control (QC) for ChronoSeq with no stimulation, all 12 Time-Tags","description":"Time-Tags were mixed 1 through 12. Data was also used for comparison with 10X Genomics 3' Chromium on K562 cells and with Single-Cell RNA-Seq negative control. Cells were not stimulated but maintained inside the ChronoSeq device for sampling. Samples were taken every 10 minutes.","dates":{"release":"2025-11-03T00:00:00Z","modification":"2026-05-27T03:13:30.92Z","creation":"2025-11-03T16:38:08.214Z"},"accession":"E-MTAB-15966","cross_references":{"ENA":["ERP183604"],"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"]}}