*** In collaboration with the NICHD Bioinformatics & Scientific Programming Core (BSPC), we have developed ‘multiome-wf’, a Snakemake workflow that can be used to transform & combine raw data from scRNA-seq, scATAC-seq and scMultiome experiments into usable results for downstream analysis. multiome-wf can be found on github , with documentation located here . ***

*** Please visit our Embryonic Mouse Brain Epigenome Atlas at the UCSC Genome browser to explore our comprehensive characterization of the transcriptome (scRNA-seq), chromatin accessibility (snATAC-seq), histone modifications (H3K4me3, H3K27me3, H3K27ac) and higher order chromatin structure (Hi-C and Capture-C) in the E12.5 mouse brain (Rhodes et al., Nature Communications 2022). ***

Datasets from Reducing methylation of histone 3.3 lysine 4 in the medial ganglionic eminence and hypothalamus recapitulates neurodevelopmental disorder phenotypes (bioRxiv, 2025):

GSE293881 → Single cell Multiome reactions for all WT & H3.3K4M homozygous E13.5 (MGE & hypothalamus) and P60 (cortex & hypothalamus) samples used in this study. Separate subseries of snRNA-seq (GSE293751) & snATAC-seq (GSE293655) datasets.

Datasets from Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles (Front Cell Neurosci, 2024):

GSE233153 → Single cell Multiome reactions for all E12.5 & E15.5 Nkx2.1-Cre;Ezh2 WT, heterozygous and homozygous samples used in this study. Separate subseries of snRNA-seq (GSE233151) and snATAC-seq (GSE233152) datasets.
GSE233190 → H3K27me3 CUT&Tag reactions of E12.5 and E15.5 MGE from Nkx2.1-Cre;Ezh2 WT, Het and Hom mouse.

Datasets from Transcriptional Heterogeneity of ventricular zone cell in the ganglionic eminences of the mouse forebrain (eLife, 2022):

GSE167013 → scRNA-seq of E12.5 WT MGE, LGE, CGE and cortex 
GSE190593 → (1) scRNA-seq of E12.5 Nes-dVenus MGE, LGE, CGE and cortex, (2) scRNA-seq of E14.5 WT MGE, LGE and CGE, (3) scRNA-seq of E14.5 Nes-dVenus MGE, LGE and CGE

Datasets from An epigenome atlas of neural progenitors within the embryonic mouse forebrain (Nat Comm, 2022):

GSE167050 → snRNA-seq and snATAC-seq of E12.5 WT MGE, LGE, CGE & cortex, and P30 Dlx6aCre;Sun1-GFP cortex & hippocampus samples used in this study. Separate subseries of E12.5 scRNA-seq (GSE167013), P30 snRNA-seq (GSE167016), E12.5 snATAC-seq (GSE167047) and P30 snATAC-seq (GSE167048) datasets.
GSE201494 → Cut&Tag and CUT&RUN reactions for E12.5 WT, MGE, LGE, CGE and cortex. Separate subseries of H3K4me3 CUT&Tag (GSE201487), H3K27me3 CUT&Tag (GSE201488) and H3K27ac CUT&RUN (GSE201400) datasets. 
GSE201186 → Hi-C reactions of E12.5 WT MGE, LGE, CGE and cortex
GSE201317 → Capture-C reactions of E12.5 WT MGE, LGE, CGE and cortex