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Effects of Nova1 Deletion on Gene Expression in Tissues and Cells

GSE212473 Mus musculus (mouse) RNA-seq (gene expression) 62 samples Submitted 2024/08/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 62 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
62 samples: 15 conditions, mostly with about 4 replicates eachGroups 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.
Paper
NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neuronsCell reports · 2023
Summary (written by the submitters)
To elucidate the function of Nova1 in neurons, especially in inhibitory neurons, gene expression profiling analysis (RNAseq, TRAP-seq) was performed using Nova1 conditional knockout mice and their primary neurons.
Published in
NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neurons
Tajima Y, Ito K, Yuan Y et al. · Cell reports 2023 · PMID 36716149 · doi:10.1016/j.celrep.2023.112050
This dataset
Open GSE212473 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 GSE212473_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 PRJNA875480 and SRA study SRP395117. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 36716149) ↗
Study design
15 conditions, mostly with about 4 replicates each
P0 TRAP, whole brain, cKO, ×6 P0 TRAP, whole brain, cHet, ×6 Hypothalamus, cKO, ×4 Hypothalamus, cHet, ×4 Periaqueductal gray, cKO, ×4 Periaqueductal gray, cHet, ×4 Caudate putamen, cHet, ×4 Substantia nigra, cHet, ×4 +9 more

Supports a between-group comparison across 60 samples.

How we read this: 15 replicated groups read from 62 sample titles; they account for 60 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

+ 22 more — browse all 62 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.