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Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution

GSE178686 Mus musculus (mouse) Single-cell RNA-seq 14 samples Submitted 2024/06/01 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 14 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
14 samples: 7 conditions, mostly in duplicateGroups 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)
Single cell RNA-Seq time-course analysis revealed in vivo mouse gastrulation and in vitro directed differentiation
This dataset
Open GSE178686 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 GSE178686_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 PRJNA740009 and SRA study SRP325099. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly in duplicate
E7.5 embryo YT_E7-5-1_S3_L ×2 E7.5 embryo YT_E7-5-2_S5_L ×2 E8.25 embryo YT_1_S1_L ×2 E8.25 embryo YT_3_S2_L ×2 E6.5 embryo YT-E1_S4_L ×2 Multiseq embryoid body experiment for D4-D8 M… ×2 Multiseq embryoid body experiment for D4-D8 M… ×2

Supports a between-group comparison across 14 samples.

How we read this: 7 replicated groups read from 14 sample titles; they account for 14 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

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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.