GEO series
Integrative single-nucleus multiomic, CUT&Tag, and bulk RNA-seq profiling of human and mouse prefrontal cortex reveals gene regulatory mechanisms of cortical development and Meis2 function
GSE325427
Homo sapiens; Mus musculus
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
34 samples
Submitted 2026/07/15
Platform GPL24676Platform GPL24247
Summary
The development of the prefrontal cortex (PFC) is governed by coordinated transcriptional and epigenomic regulatory programs. To comprehensively characterize these processes, we generated an integrative multi-modal dataset combining single-nucleus multiomic (snRNA-seq and snATAC-seq), CUT&Tag, and bulk RNA-seq data from human and mouse PFC. Single-nucleus multiomic data from human mid-fetal dorsolateral prefrontal cortex (dlPFC) samples and mouse postnatal day 1 (P1) medial prefrontal cortex (mPFC) and motor cortex (MC) and provide matched gene expression and chromatin accessibility profiles across diverse cell types. Complementary CUT&Tag experiments profiling key transcription factors (RARA, RARB, RXRG, MEIS2) and histone modifications (H3K27ac, H3K4me3) further define regulatory elements and transcriptional control landscapes. To investigate the functional role of Meis2, bulk RNA-seq was performed on mouse P0 medial prefrontal cortex (mPFC) from control and Meis2 conditional knockout (cKO) samples. These data enable the identification of gene expression changes associated with Meis2 perturbation. Together, this integrated dataset provides a resource for studying gene regulatory networks underlying cortical development and for linking transcription factor activity to downstream gene expression programs across species.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE325427_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 34 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1438418 and SRA study SRP684386. Searching any of these in the dataset finder brings you back here.
Study design
8 conditions, mostly in duplicate
RNA-seq of CTR mouse P0 mPFC sample MP0PFC ×3
RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0… ×3
H3K27ac CUT&Tag of human mid-fetal dlPFC DFC ×2
H3K4me3 CUT&Tag of human mid-fetal dlPFC DFC ×2
MEIS2 CUT&Tag of human mid-fetal dlPFC DFC ×2
RARA CUT&Tag of human mid-fetal dlPFC DFC ×2
RARB CUT&Tag of human mid-fetal dlPFC DFC ×2
RXRG CUT&Tag of human mid-fetal dlPFC DFC ×2
+16 more
Supports a between-group comparison across 18 samples.
8 replicated groups read from 34 sample titles; they account for 18 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9603485 snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H421DFCm2
- GSM9603486 snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H421DFCm2
- GSM9603487 snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H431DFCm
- GSM9603488 snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H431DFCm
- GSM9603489 snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H596DFCm1
- GSM9603490 snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H596DFCm1
- GSM9603491 snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H429DFCm
- GSM9603492 snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H429DFCm
- GSM9603505 snMultiome(snATAC-seq) of WT mouse P1 motor cortex sample MfP1MCm
- GSM9603506 snMultiome(snRNA-seq) of WT mouse P1 motor cortex sample MfP1MCm
- GSM9603507 snMultiome(snATAC-seq) of WT mouse P1 mPFC sample MfP1PFm
- GSM9603508 snMultiome(snRNA-seq) of WT mouse P1 mPFC sample MfP1PFm
- GSM9603509 snMultiome(snATAC-seq) of WT mouse P1 motor cortex sample MmP1MCm
- GSM9603510 snMultiome(snRNA-seq) of WT mouse P1 motor cortex sample MmP1MCm
- GSM9603511 snMultiome(snATAC-seq) of WT mouse P1 mPFC sample MmP1PFm
- GSM9603512 snMultiome(snRNA-seq) of WT mouse P1 mPFC sample MmP1PFm
- GSM9603513 RNA-seq of CTR mouse P0 mPFC sample MP0PFC1
- GSM9603514 RNA-seq of CTR mouse P0 mPFC sample MP0PFC2
- GSM9603515 RNA-seq of CTR mouse P0 mPFC sample MP0PFC3
- GSM9603516 RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0PFE1
- GSM9603517 RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0PFE2
- GSM9603518 RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0PFE3
- GSM9829202 H3K27ac CUT&Tag of human mid-fetal dlPFC DFC1
- GSM9829203 H3K4me3 CUT&Tag of human mid-fetal dlPFC DFC1
- GSM9829204 MEIS2 CUT&Tag of human mid-fetal dlPFC DFC1
- GSM9829205 RARA CUT&Tag of human mid-fetal dlPFC DFC1
- GSM9829206 RARB CUT&Tag of human mid-fetal dlPFC DFC1
- GSM9829207 RXRG CUT&Tag of human mid-fetal dlPFC DFC1
- GSM9829208 H3K27ac CUT&Tag of human mid-fetal dlPFC DFC2
- GSM9829209 H3K4me3 CUT&Tag of human mid-fetal dlPFC DFC2
- GSM9829210 MEIS2 CUT&Tag of human mid-fetal dlPFC DFC2
- GSM9829211 RARA CUT&Tag of human mid-fetal dlPFC DFC2
- GSM9829212 RARB CUT&Tag of human mid-fetal dlPFC DFC2
- GSM9829213 RXRG CUT&Tag of human mid-fetal dlPFC DFC2
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