{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Koen Deserranno"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15047"],"description":["Single cell RNA-profiling in tandem with short-read sequencing (SR-scRNA-seq) has revolutionized the field of transcriptomics, permitting a highly granular view on cellular blood and tissue composition and the construction of human cell atlases. However, discrimination between various transcript isoforms remains challenging. Here we developed single cell long-read isoform sequencing (scLIS-seq), a scRNA-seq workflow based on Smart-seq3xpress (SS3X) cDNA generation and Oxford Nanopore Technologies PromethION sequencing. Using scLIS-seq, we profiled the long-read transcriptomes of Jurkat and HEK293T cells and compared its performance to SS3X starting from the identical cDNA. This dataset refers to the raw and processed data of the Smart-seq3xpress and scLIS-seq experiments of the Jurkat and HEK293T cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - scLIS-seq, as described in https://doi.org/10.21203/rs.3.rs-6217988/v1.","Sample Collection - Jurkat T lymphoblasts were first blocked with anti-human FcR (Miltenyi, #130-059-901) for 10 minutes at room temperature to avoid non-specific binding of antibodies. Next, these cells were incubated with antibodies against CD3 (clone UCHT1, BioLegend cat. Nr. 300440, FITC, dilution: 1:200) and TCR α/β (clone IP26, BioLegend cat. Nr. 306718, APC, dilution: 1:200). Both Jurkat and HEK293T cells were washed using phosphate buffered saline (PBS, Gibco), and finally were resuspended in PBS. Propidium iodide staining was performed to mark dead cells. Additionally, for Jurkat, gating for living CD3+TCRαβ+ cells was performed. The cells were sorted as single cells into 384-well Armadillo plates plate (Thermo Fisher Scientific, Waltham, MA, USA)  containing 0.3 µL SS3X lysis buffer and 3 µL of 5 cSt silicon oil overlay (Merck) per well. Sorting was performed using BD FACSAria Fusion (BD Biosciences) for Jurkat and BD FACSAria II (BD Biosciences) for HEK293T with a 70-µm nozzle. After sorting, each plate was immediately sealed, centrifuged, and stored at -80 °C upon further processing.","Nucleic Acid Extraction - Cells were directly lysed in 0.3 µL of Smart-seq3xpress lysis buffer, without separate RNA-extraction.","Library Construction - Smart-seq3xpress, as described by Hagemann-Jensen et al. (V2 version, accessible from https://www.protocols.io/view/smart-seq3xpress-yxmvmk1yng3p/v2)","Sequencing - Sequencing of the Smart-seq3xpress libraries was performed using Element AVITI - PE150.","Sequencing - Oxford Nanopore Technologies PromethION - Library preparation using SQK-NBD114.24 kit - R10.4.1 flow cells"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The raw Nanopore sequencing data was basecalled using Dorado (v0.8.3) to convert the .pod5 files to .fastq files. To construct the count matrices for both Jurkat and HEK293T, adapted versions of wf-single-cell (v2.0.3) and scywalker (v0.110.0) were run. The exact adaptations are added as Supplementary Materials to the manuscript.","Data Transformation - The raw Smart-seq3xpress AVITI sequencing data of Jurkat and HEK293T was processed using zUMIs (v.2.9.7e). The Ensembl GRCh38 release 111 was used as a reference."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["BD FACSAria Fusion","Element AVITI","PromethION"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Plate-based long-read single cell gene- and isoform transcriptome profiling using scLIS-seq"],"pubmed_authors":["Filip Van Nieuwerburgh","Koen Deserranno","Deserranno Koen, Callens Elise, Berrevoet Danique, Deforce Dieter, Van Nieuwerburgh Filip"],"additional_accession":[]},"is_claimable":false,"name":"Plate-based long-read single cell gene- and isoform transcriptome profiling using scLIS-seq","description":"Single cell RNA-profiling in tandem with short-read sequencing (SR-scRNA-seq) has revolutionized the field of transcriptomics, permitting a highly granular view on cellular blood and tissue composition and the construction of human cell atlases. However, discrimination between various transcript isoforms remains challenging. Here we developed single cell long-read isoform sequencing (scLIS-seq), a scRNA-seq workflow based on Smart-seq3xpress (SS3X) cDNA generation and Oxford Nanopore Technologies PromethION sequencing. Using scLIS-seq, we profiled the long-read transcriptomes of Jurkat and HEK293T cells and compared its performance to SS3X starting from the identical cDNA. This dataset refers to the raw and processed data of the Smart-seq3xpress and scLIS-seq experiments of the Jurkat and HEK293T cells.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:19.833Z","creation":"2025-04-22T16:05:57.777Z"},"accession":"E-MTAB-15047","cross_references":{"ENA":["ERP170176"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}