Single cell methylation, RNA and ATAC seq data from C57BL/6J and DBA/2J strains

Each file comes from a different cell type identified by clustering. The filenames indicate the cell type where Exc- refers to excitatory neurons and Inh- refers to inhibitory neurons. Non neuronal types are astrocytes and oligodendroglia (ODC). Data are for methylated CpG sites in the mouse genome (non CpG methylation is not included)

The files have column headings to be interpreted as follows:

chr  - chromosome

pos - position on the chromosome in basepairs 

context - a 5bp sequence at the centre of which is the CpG

density - the local density of CpG sequences in a 2Kb segment  

b6.var  - C57BL/6J  sequence at this site 

d2.var - DBA/2J sequence at this site 

b6.me - C57BL/6J number of methylated reads

b6.cov - C57BL/6J  total read coverage

d2.me - DBA/2J number of methylated reads

d2.cov - DBA/2J total read coverage

gene -  gene name at this site

cgi - presence of a CpG island

tss - presence of a transcriptional start site

rna.logp - negative logP of the RNA analysis from DESeq2 comparing C57BL/6J and DBA/2J transcript abundance

rna.counts  - read counts of snRNA seq, combined values for  C57BL/6J and DBA/2J strains

rna.log2fold - log2 fold difference in  C57BL/6J and DBA/2J transcript abundance from DESeq2 

atac.logp - negative logP of the ATACseq analysis from DESeq2 comparing C57BL/6J and DBA/2J transcript abundance

atac.log2fold  - log2 fold difference in  C57BL/6J and DBA/2J ATACseq from DESeq2 

atac.counts - read counts of ATACseq, combined values for  C57BL/6J and DBA/2J strains

states -  a set of ‘universal chromatin state annotations’ of the mouse genome based on over 900 datasets from various cell and tissue types (Vu and Ernst, 2023)