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Transcriptome analysis of single cells from the mouse dentate gyrus [C1]

GSE95752 Mus musculus (mouse) Single-cell RNA-seq 2303 samples Submitted 2017/12/13 Platform GPL13112
At a glance

Single-cell RNA-seq · mouse · 2303 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
2303 samples: 103 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.
Summary (written by the submitters)
RNA sequencing was performed on 2303 single cells from dentate gyrus of CD-1 and hGFAP-GFP reporter mice, sampled at 17 time points from P8 to P68, with the aim of delineating the distinct cellular states along the granule cell lineage.
This dataset
Open GSE95752 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 GSE95752_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 PRJNA378269 and SRA study SRP101462. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29335606) ↗
Study design
103 conditions, mostly with about 4 replicates each
1772092282_B ×8 1772092289_C ×8 1772092266_A ×7 1772092269_C ×7 1772092290_B ×7 1772092260_A ×6 1772092260_H ×6 1772092269_B ×6 +104 more

Supports a between-group comparison across 391 samples.

How we read this: 103 replicated groups read from the first 400 of 2303 sample titles; they account for 391 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

+ 2263 more — browse all 2303 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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