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C57BL6 Substrain Differences in Hippocampal-Dependent Learning and Transcriptome

GSE291439 Mus musculus (mouse) RNA-seq (gene expression) 72 samples Submitted 2026/07/01 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 72 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
72 samples: 72 samples, each with a distinct title — no replicated groupsGroups 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)
Here, we evaluated B6J and B6NJ substrains in a fear conditioning paradigm with varied conditioned stimulus-unconditioned stimulus pairings to assess if the strength of learning varies between substrains. For all number of pairings, B6NJ showed enhanced contextual freezing compared to B6J.
Read the full summary ↓
To investigate baseline and learning-induced changes in hippocampal transcriptome that may underlie the observed behavioral differences between B6J and B6NJ, dorsal and ventral hippocampi were analyzed for RNAsequencing from B6J and B6NJ male mice from three groups: direct from home cage, 30 minutes after 2-pairings of shock and cue, 30 minutes after 2 exposures to cue alone. RNASeq pathway and network analysis identified several genes related to BDNF signaling that could contribute to the differences in levels contextual fear learning observed. Together, these behavioral and transcriptomic findings confirm differences in conditioned fear between the commonly used B6 substrains B6J and B6NJ and suggest that hippocampal transcriptome differences related to BDNF may contribute to differences in learning
This dataset
Open GSE291439 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 GSE291439_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1233600 and SRA study SRP568898. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
72 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 72 sample titles: 72 distinct titles with little repetition. 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

+ 32 more — browse all 72 samples with per-sample file links →

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.