User profiles for C. Ziegenhain

Christoph Ziegenhain

Karolinska Institutet
Verified email at ki.se
Cited by 4881

Quantitative single-cell transcriptomics

C Ziegenhain, B Vieth, S Parekh… - Briefings in …, 2018 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of
biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over …

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

E Mereu, A Lafzi, C Moutinho, C Ziegenhain… - Nature …, 2020 - nature.com
Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the
transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of …

[HTML][HTML] Comparative analysis of single-cell RNA sequencing methods

C Ziegenhain, B Vieth, S Parekh, B Reinius… - Molecular cell, 2017 - cell.com
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and
medical questions. However, systematic comparisons of the performance of diverse scRNA-…

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

…, M Friedrich, L Rad, M Barenboim, C Ziegenhain… - Nature, 2018 - nature.com
C for 24 min), treated with pepsin solution (at 37 C for 8 min) and denatured by a heat treatment
step at 80 C … by co-denaturing at 75 C for 10 min and by incubating at 37 C overnight in a …

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

M Hagemann-Jensen, C Ziegenhain, P Chen… - Nature …, 2020 - nature.com
… ) was added to each well and incubated at 3 min 72 C; 30 s at 95 C; 12 cycles of (10 s at
95 C; 30 s at 55 C; 30 s at 72 C); and 5 min at 72 C, in a thermal cycler. For the experiments …

[PDF][PDF] Characterization of rare, dormant, and therapy-resistant cells in acute lymphoblastic leukemia

S Ebinger, EZ Özdemir, C Ziegenhain, S Tiedt… - Cancer cell, 2016 - cell.com
… (E) Similar experiment as in (C), except that the donor mouse was fed with BrdU in the last
7 … (C) Principal component analysis of the 500 most variable genes in all 50 single cells. (D) …

[PDF][PDF] zUMIs-A fast and flexible pipeline to process RNA sequencing data with UMIs

S Parekh, C Ziegenhain, B Vieth, W Enard… - …, 2018 - academic.oup.com
… (C) Comparison of the total number of UMIs per cell derived from different counting methods
to “unfiltered” counts. (D) Violin plots of gene-wise dispersion estimates with different quality …

[HTML][HTML] A systematic evaluation of single cell RNA-seq analysis pipelines

B Vieth, S Parekh, C Ziegenhain, W Enard… - Nature …, 2019 - nature.com
c The analysis pipeline: The simulated data sets are then analysed using combinations of
four count matrix preprocessing, seven normalisation and four DE approaches. The evaluation …

[HTML][HTML] The impact of amplification on differential expression analyses by RNA-seq

S Parekh, C Ziegenhain, B Vieth, W Enard… - Scientific reports, 2016 - nature.com
… In panel (c), we plot our estimates of the marginal power against the number of PCR-cycles
for each dataset. Error bars are standard deviation to the mean marginal power over 100 …

[HTML][HTML] Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

JW Bagnoli, C Ziegenhain, A Janjic, LE Wange… - Nature …, 2018 - nature.com
… PCR was cycled as given: 3 min at 98 C for initial denaturation followed by 15 cycles of
15 s at 98 C, 30 s at 65 C, 4 min at 68 C. Final elongation was performed for 10 min at 72 C. …