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Series GSE266160 Query DataSets for GSE266160
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
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
 
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.
 
Contributor(s) Moro G, Mallona I, Robinson MD, Brunner E, Basler K
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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
Organization name University of Zurich
Department DMLS
Lab Prof. Dr. Konrad Basler
Street address Winterthurerstrasse 190
City Z├╝rich
ZIP/Postal code 8057
Country Switzerland
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM8241647 Colon, rockroi multimodal
GSM8241648 Colon, unmod unimodal
GSM8241649 Colon, rockroi unimodal
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
Relations
BioProject PRJNA1106036

Download family Format
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Supplementary file Size Download File type/resource
GSE266160_RAW.tar 1.1 Gb (http)(custom) TAR (of BW, CSV, MTX, TSV)
GSE266160_custom_regions_pdgfra.gtf.gz 529 b (ftp)(http) GTF
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Raw data are available in SRA

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