The Takara ICELL8 5184 nano-well chip was used with the full-length SMART-Seq ICELL8 Reagent Kit. Nuclei suspensions were fluorescent-labelled with Hoechst 33342 for 15 min prior to their dispensing into the Takara ICELL8 5184 nano-well chips. Cell Select Software (Takara Bio) was used to visualize and select wells containing single nuclei. Nine 5184 nano-wells chips were used for all samples and 11 084 nuclei were processed for data analysis. Specifically, after quality control, 3416 nuclei were used for primary PDAC, 3037 for PDX and 4631 for organoids respectively. cDNA synthesis and library preparation were done according to description in previous study (16 (link)). Libraries were sequenced on the HiSeq 4000 (Illumina) to obtain on average ∼ 0.3 Mio reads per nuclei (SE; 50 bp).
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Single-nucleus RNA-seq of PDAC samples
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Corresponding Organization : Universitätsmedizin Göttingen
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Variable analysis
independent variables
- Fluorescent labeling of nuclei suspensions with Hoechst 33342
- Number of nuclei processed for data analysis
- Number of nuclei used for primary PDAC, PDX, and organoids after quality control
- Takara ICELL8 5184 nano-well chip used for all samples
- Cell Select Software (Takara Bio) used to visualize and select wells containing single nuclei
- CDNA synthesis and library preparation methods
- Sequencing on the HiSeq 4000 (Illumina) to obtain on average ∼ 0.3 Mio reads per nuclei (SE; 50 bp)
- No positive or negative controls were explicitly mentioned in the provided information.
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