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Transcriptome analysis of single cells from the developing mouse dentate gyrus

GSE104323 Mus musculus (mouse) Single-cell RNA-seq 232 samples Submitted 2017/12/13 Platform GPL21103
At a glance

Single-cell RNA-seq · mouse · 232 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
232 samples: 157 distinct titles, 24 of them repeatedGroups 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 24185 single cells from dentate gyrus of CD-1, C57Bl/6, or hGFAP-GFP reporter mice, sampled at ages ranging from embryonal day 16.5 to postnatal day 132, with the aim of comparing peri- and postnatal neurogenesis in the dentate gyrus
This dataset
Open GSE104323 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 GSE104323_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 PRJNA412365 and SRA study SRP118985. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29335606) ↗
Study design
157 distinct titles, 24 of them repeated
P0,CD-1,Immature-Py ×12 P132,hGFAP-GFP,GC-adult ×11 E16.5,CD-1,Immature-Py ×8 P18,CD-1,GC-juv ×8 P5,CD-1,Immature-GC ×7 P23,CD-1,GC-juv ×6 P132,hGFAP-GFP,Astro-adult ×4 P19,C57Bl/6,GC-juv ×4 +16 more

How we read this: Read from 232 sample titles: 157 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

+ 192 more — browse all 232 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq 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.