{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR288/092/SRR28817192/SRR28817192_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR288/093/SRR28817193/SRR28817193_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR288/093/SRR28817193/SRR28817193_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR288/092/SRR28817192/SRR28817192_2.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Prof. Dr. Konrad Basler, DMLS, University of Zurich"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA1105052"],"long_description":["Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest Overall design: RoCK and ROI is based on barcoded beads of the BD Rhapsody platform. For RoCKseq specific capture, TSO oligos on BD Rhapsody beads are modified with a/ multiple capture sequence(s) specific to transcripts of interest. ROIseq, on the other hand, is based on specific primers which are spiked in during library generation, directing reads to regions of interest (ROIs). Multiple scRNAseq experiments were performed on several biological samples to validate RoCK and ROI. To validate RoCK and ROI library generation, scRNAseq experiments were performed on a mix of murine and human cell lines expressing eGFP or tdTomato respectively. As a further validation of RoCK and ROI, epithelial and mesenchymal cells from a transgenic mouse strain (B6.129S4-Pdgfratm11(EGFP)Sor/J) were used."],"repository":["ENA"],"name_synonyms":["Ribonucleic, d230, Procedures, Transcriptome Profile, region or site annotation, Gene Expression Profile, Gene, dTAFII250, Profiles, CG10393, DmelCG9774, EfW1, dmTAF[[II]]230, Tft, method, Techniques, Drok, dmTAF1, Taf230, Method, DmelCG10393, method used in an experiment, Amos, Gene Products, Studies, DRhk, Non Polyadenylated, Technique, RNA Gene Products, TAF250, ROCK, Taf200, positional, dTAF[[II]]250, TFIID TAF250, cel, asolo, cell, Profile, Taf1p, Signatures, Non-Polyadenylated RNA, Study, dTAF250, Methodological Studies, Expression Signature, Transcriptomes, TAF, RNA, dTAF[[II]]230, TAF[[II]]250, Transcriptome, CG9774, ribose nucleic acid, bHLHa10, Expression Profiles, ribonucleic acids, TAF200, l(3)84Ab, RNS, BG:DS00004.13, TAFII-250, Procedure, TAF250/230, Cell, dTAF230, whole transcriptome, Gene Expression, Rock, TAFII250, p230, yeast nucleic acid, Roi, Ribonukleinsaeure, Expression Signatures, Gene Expression Signatures, ROK, ROCK-1, Rok, TAF[[II]]250/230, sequence, TFIID, pentosenucleic acids, RhoK, Ribonucleic acids, rolo, Gene Expression Signature, Expression Profile, Transcriptome Profiles, Taf[[II]]250, ribonucleic acid, Acid, ROCK1, drok, TAF[[II]]230, positional polypeptide feature, DROK, DRok, Non Polyadenylated RNA, Non-Polyadenylated, Rhk, TAF[II]250, Ribonucleic Acid, Methodological, CG17603, TAF[[II]], Methodological Study, plan specification, dRok, dROK, DmelCG17603, Taf250, SR3-5, Gene Expression Profiles, primary structure of sequence macromolecule., Signature, ROKalpha/beta, TAF230, TAF1"],"description_synonyms":["Ribonucleic, d230, Procedures, Transcriptome Profile, region or site annotation, Gene Expression Profile, Gene, dTAFII250, Profiles, CG10393, DmelCG9774, EfW1, dmTAF[[II]]230, Tft, method, Techniques, Drok, dmTAF1, Taf230, Method, DmelCG10393, method used in an experiment, Amos, Gene Products, Studies, DRhk, Non Polyadenylated, Technique, RNA Gene Products, TAF250, ROCK, Taf200, positional, dTAF[[II]]250, TFIID TAF250, cel, asolo, cell, Profile, Taf1p, Signatures, Non-Polyadenylated RNA, Study, dTAF250, Methodological Studies, Expression Signature, Transcriptomes, TAF, RNA, dTAF[[II]]230, TAF[[II]]250, Transcriptome, CG9774, ribose nucleic acid, bHLHa10, Expression Profiles, ribonucleic acids, TAF200, l(3)84Ab, RNS, BG:DS00004.13, TAFII-250, Procedure, TAF250/230, Cell, dTAF230, whole transcriptome, Gene Expression, Rock, TAFII250, p230, yeast nucleic acid, Roi, Ribonukleinsaeure, Expression Signatures, Gene Expression Signatures, ROK, ROCK-1, Rok, TAF[[II]]250/230, sequence, TFIID, pentosenucleic acids, RhoK, Ribonucleic acids, rolo, Gene Expression Signature, Expression Profile, Transcriptome Profiles, Taf[[II]]250, ribonucleic acid, Acid, ROCK1, drok, TAF[[II]]230, positional polypeptide feature, DROK, DRok, Non Polyadenylated RNA, Non-Polyadenylated, Rhk, TAF[II]250, Ribonucleic Acid, Methodological, CG17603, TAF[[II]], Methodological Study, plan specification, dRok, dROK, DmelCG17603, Taf250, SR3-5, Gene Expression Profiles, primary structure of sequence macromolecule., Signature, ROKalpha/beta, TAF230, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing I","description":"RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing I","dates":{"last_updated":"2025-09-24","first_public":"2024-05-11"},"accession":"PRJNA1105052","cross_references":{"GEO":["GSE265962"]}}