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Single-cell Epi2-seq

This is the repository accompanying the Manuscript Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenetic maintenance. It contains links to all the (raw) sequencing data, FACS index data as well as information about the preprocessing and downstream analyses.

Data availability

Single-cell Epi2-seq data

Raw data for combined methylation and histone profiling have been deposited at the Gene Expression Omnibus (accession GSE232637).

RPE1-hTERT WGBS data

Raw WGBS data have been deposited at the Gene Expression Omnibus (accession GSE232637).

K562 whole-genome bisulfite sequencing (WGBS)

Data were downloaded from ENCODE:

K562 ChIP-Seq data

  1. H3K27me3 dataset
  1. H3K36me3 dataset
  1. H3K9me3 dataset

K562 ChIC data

Count tables for single-cell sortChIC data from Zeller et al. were downloaded from GEO repository GSE164779.

Preprocessing

Preprocessing of fastq.gz files was performed using the Package SingleCellMultiOmics developed by Buys de Barbanson. The software package is available on github.

Code for figures

All code to produce the figures in the manuscript can be found in the subdirectory code.

Adapter sequences

Supplementary files containing all adapter and oligo sequences used for sequencing library preparation are summarized in three supplementary tables in the subdirectory tables.

Index Data

FACS plots for the experiments in RPE-1 hTERT Fucci cells where deposited in the subdirectory facs_plots. The subfolder index_data contains FACS parameters for every single cell, file names refer to the data available via GEO.

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Manuscript for single-cell Epi2-Seq

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