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Single-nucleus RNA-seq of mouse cortex during mid-gestation pregnancy

GSE325586 Mus musculus Expression profiling by high throughput sequencing 4 samples Submitted 2026/03/25 Platform GPL34475
Summary
Single-nucleus RNA sequencing (snRNA-seq) was performed on cortical tissue from non-pregnant and pregnant (embryonic day E13.5) female C57BL/6JRj mice (~12 weeks old) to characterize transcriptomic changes in brain cell populations during pregnancy. This dataset accompanies the study "The lipidomic architecture of the mouse brain" (Fusar Bassini et al.), in which MALDI mass spectrometry imaging was used to map 172 lipids across the adult mouse brain. The snRNA-seq data were generated to investigate cell type-specific transcriptomic changes in the cortex of pregnant mice, complementing the spatial lipidomics findings. Nuclei were isolated from microdissected cortex using NP-40 lysis and iodixanol gradient purification, and libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3' v4 (GEMX) kit. Sequencing was performed on an Element Biosciences AVITI24 system to a depth of ~50,000 reads per nucleus. Between 6,357 and 6,932 nuclei were recovered per sample, with a median of ~3,900-4,500 genes per nucleus.
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Direct links to NCBI, no account and no request form: the whole study as GSE325586_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 4 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1440509 and SRA study SRP685553. Searching any of these in the dataset finder brings you back here.

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