← BioTransfer GEO Dataset Finder
GEO series

Trancriptome profiling of medial frontal cortices of P28 offspring from breeding of Dnmt3l conditional knockin and Emx1-cre mice

GSE268951 Mus musculus (mouse) Non-coding RNA profiling 24 samples Submitted 2024/08/31 Platform GPL21493Platform GPL24247
At a glance

Non-coding RNA profiling · mouse · 24 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Mus musculus (mouse)
Samples
24 samples: 3 × A vs 3 × B vs 3 × C vs 3 × DGroups 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)
The objective of the study was to examine the gene expression changes in the medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, strain of C57BL/6J. There were 12 samples in total- A-1, A-2, A-3, B-1, B-2, B-3, C-1, C-2, C-3, D-1, D-2, and D-3. A-1 to A-3 and B-1 to B-3 were medial frontal cortices from the male and female Emx1-cre mice respectively, which were used as the control groups (CON).
Read the full summary ↓
C-1 to C-3 and D-1 to D-3 were medial frontal cortices from the male and female Dnmt3l overexpression mice respectively, which were used as the experimental groups (OE). The total RNA of each sample was extracted from the medial frontal cortices by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. There were two types of libraries: the circRNA, mRNA, and lncRNA were all constructed by removing rRNA (one library, three types of RNA were analyzed together), and the insert fragment was about 300bp; the small RNA was constructed and analyzed separately, mainly microRNA of about 22bp. Results: among 119414 cleaned mRNAs, 3015 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). The differential expressed genes distributed in all chromosomes. Functional annotation with GO and KEGG enrichment revealed the top functional groups including ATP binding, zinc ion binding, glutamatergic synapse, dopaminergic synapse, MAPK signaling pathway, and PI3K-Akt signaling pathway. Among 23698 lncRNAs, 658 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 10673 circRNAs, 49 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 1821 microRNAs, 101 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold).
This dataset
Open GSE268951 in finder → Find more mouse 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 GSE268951_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 ↗

Also filed as BioProject PRJNA1119493 and SRA study SRP511456. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × A vs 3 × B vs 3 × C vs 3 × D

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 24 sample titles; they account for 12 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 datasets in GEO →

Share this dataset

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.