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Cancer Genomics Center


Single cell RNA sequencing (scRNA-seq) service

The CGC provides single cell RNA sequencing service using the 10X Genomics Chromium system combined with the Illumina sequencing machine. The 10X system makes it possible to profile thousands of single cells. Here are web links introducing scRNA-seq from 10X Genomics:

Sample preparation guidelines

ServiceSample typeMinimum amountMinimum cell viability
scRNA-seq Cell 106 85%

*For more details on sample preparation, please contact us.
*Please use Qubit to measure DNA/RNA concentration.
*Please provide Bioanalyzer results for your sample if it is available.

Service workflow

Service Workflow Diagram scRNA-seq

Analysis pipeline (general purpose)

Analysis Pipeline scRNA-seq Diagram
Related publications from our team:

  1. Braga FAV, Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, et al. A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease. bioRxiv. 2019.
  2. Wolf FA, Alexander Wolf F, Hamey FK, Plass M, Solana J, Dahlin JS, et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology. 2019.
  3. Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, et al. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat Commun. 2019.
  4. Eraslan G, Simon LM, Mircea M, Mueller NS, Theis FJ. Single-cell RNA-seq denoising using a deep count autoencoder. Nat Commun. 2019.
  5. Krendl C, Shaposhnikov D, Rishko V, Ori C, Ziegenhain C, Sass S, et al. GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency. PNAS. 2017.
  6. Angerer P, Simon L, Tritschler S, Alexander Wolf F, Fischer D, Theis FJ. Single cells make big data: New challenges and opportunities in transcriptomics. Current Opinion in Systems Biology. 2017.
  7. Cao Y, Zhu J, Jia P, Zhao Z. scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells. Genes. 2017.