Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS+

Xiufei Chen^1,2,3,10, Jingfei Cheng^2,3,10, Linzhen Kong^2,3,10, Xiao Shu^2,3, Haiqi Xu^2,3, Masato Inoue^2,3, Marion Silvana Fernández Berroca^l4, Dagny Sanden Døskeland⁴, Magnar Bjørås^4,5,6, Shivan Sivakumar^7,8, Yibin Liu^9,* , Jing Ye^4,* , Chun-Xiao Song^2,3,*

¹ Department of Central Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo 315010, China

² Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK. OX3 7FZ.

³ Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK. OX3 7FZ.

⁴ Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.

⁵ Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, 0424, Norway.

⁶ Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.

⁷ The Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT.

⁸ Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK. OX3 7FY.

⁹ College of Chemistry and Molecular Sciences, and Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China.

¹⁰ These authors contributed equally.

^* Corresponding authors. Email: liuyibin@whu.edu.cn, jing.ye@ntnu.no, and chunxiao.song@ludwig.ox.ac.uk.

data preprocessing

preprocess/mESC/configure.yaml
preprocess/mESC/lowinput_analysis.smk
preprocess/mESC/mESC_sccaps.smk

preprocess/t_cell/configure.yaml
preprocess/t_cell/sctaps.smk
preprocess/t_cell/standard_taps.smk

preprocess/mouse_hippocampus/configure.yaml
preprocess/mouse_hippocampus/nd_taps_convert_call.py
preprocess/mouse_hippocampus/nd_taps_extract_parallel.py
preprocess/mouse_hippocampus/sccaps.smk

Code for figures

Fig1:
figs/fig1_cd8t_cell_analysis.sh # Bash script to generate input data for plotting
figs/fig1_cd8t_cell.r # R script to generate the figure
Fig2:
figs/fig2_mouse_hippocampus_analysis.sh # Bash script to generate input data for plotting
figs/fig2_mouse_hippocampus.r # R script to generate the figure
FigS1:
figs/lowinput_archive.r
FigS3:
figs/revision.r
FigS4:
figs/sc_archive.r
figs/revision.r
FigS5:
figs/figure2.r
figs/fig1_cd8t_cell.r
FigS7:
figs/fig2_mouse_hippocampus.r