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Effects of CRISPR-mediated knockout of Mitf, Tfe3 and Tfeb on the transcriptome of mouse BMDMs from WT and Grn KO animals [hex001130]

GSE327962 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/07/20 Platform GPL34328
At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
16 samples: 4 × WT; Rosa26; vs 4 × WT; Mitf_Tfe3_Tfeb; vs 4 × GrnKO; Rosa26; vs 4 × GrnKO; Mitf_Tfe3_Tfeb;Groups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Previous single-cell RNA sequencing of microglia from aged WT and Grn KO mice revealed a microglial subset with transcriptomic signatures that were highly specific to Grn KO. Further epigenetic analysis demonstrated that these signatures were likely regulated by Mitf/Tfe family transcription factors. To investigate the necessity of these transcription factors in mediating the Grn KO transcriptomic response, we turned to an experimental in vitro validation.
Read the full summary ↓
A multiplexed CRISPR approach was used to knockout Mitf, Tfe3 and Tfeb in BMDMs from WT or Grn KO mice. 10 days post-CRISPR, bulk RNA sequencing was performed to analyze the transcriptional profiles. These profiles identified the expected enrichment of Grn KO-specific genes in BMDMs from Grn KO mouse background. Strikingly, the levels of many of these genes were reversed with knockout of Mitf, Tfe3 and Tfeb.
This dataset
Open GSE327962 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE327962_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1453394 and SRA study SRP691718. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × WT; Rosa26; vs 4 × WT; Mitf_Tfe3_Tfeb; vs 4 × GrnKO; Rosa26; vs 4 × GrnKO; Mitf_Tfe3_Tfeb;

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.