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| Status |
Public on May 07, 2024 |
| Title |
RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing III |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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
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| 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.
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| Contributor(s) |
Moro G, Mallona I, Robinson MD, Brunner E, Basler K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Apr 29, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Giulia Arianna Moro |
| E-mail(s) |
giulia.moro2@uzh.ch
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| Organization name |
University of Zurich
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| Department |
DMLS
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| Lab |
Prof. Dr. Konrad Basler
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| Street address |
Winterthurerstrasse 190
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| City |
Zürich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE266161 |
RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing |
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| Relations |
| BioProject |
PRJNA1106036 |
