Table 1.

Cell-specific transcripts identified from open chromatin.

Cell type	Protein coding	lncRNA	microRNA
Neuronal	4075	3417	87
Glutamatergic	807	1123	8
GABAergic	834	698	12
non-Neuronal	6289	4485	89
Oligodendrocyte	2318	1386	25
Microglia/astrocytes	1887	1957	33

To infer the transcriptome from chromatin accessibility, genes were linked to cell-specific open chromatin regions by direct overlap of the TSS. “Neuronal” is not simply the sum of “Glutamatergic” and “GABAergic”, as the latter two exclude chromatin that are not specific to either neuronal subtype (Methods). Likewise, “non-Neuronal” is not the sum of the two constituent cell subtypes. For microRNA host genes, only genes encoding one or more conserved microRNA were considered.