A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain.
Single-cell RNA-seq · mouse · 32 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
- 32 samples: 12 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.
- Paper
- A single-cell transcriptomic map of the developing Atoh1 lineage identifies neural fate decisions and neuronal diversity in the hindbrainDevelopmental cell · 2024
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE233966_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA979116 and SRA study SRP440568. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 32 sample titles; they account for 24 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.
- GSM7438094 E9.5, GFP-only, replicate 1 E9.5, GFP-only,
- GSM7438095 E9.5, GFP-only, replicate 2 E9.5, GFP-only,
- GSM7438096 E10.5, GFP-only, replicate 1 E10.5, GFP-only,
- GSM7438097 E10.5, GFP-only, replicate 2 E10.5, GFP-only,
- GSM7438098 E11.5, GFP/TdTom, replicate 1 E11.5, GFP/TdTom,
- GSM7438099 E11.5, GFP/TdTom, replicate 2 E11.5, GFP/TdTom,
- GSM7438100 E11.5, TdTom-only, replicate 1 E11.5, TdTom-only,
- GSM7438101 E11.5, TdTom-only, replicate 2 E11.5, TdTom-only,
- GSM7438102 E12.5, GFP/TdTom, replicate 1 E12.5, GFP/TdTom,
- GSM7438103 E12.5, GFP/TdTom, replicate 2 E12.5, GFP/TdTom,
- GSM7438104 E12.5, TdTom-only, replicate 1 E12.5, TdTom-only,
- GSM7438105 E12.5, TdTom-only, replicate 2 E12.5, TdTom-only,
- GSM7438106 E13.5, GFP/TdTom, replicate 1 E13.5, GFP/TdTom,
- GSM7438107 E13.5, GFP/TdTom, replicate 2 E13.5, GFP/TdTom,
- GSM7438108 E13.5, TdTom-only, replicate 1 E13.5, TdTom-only,
- GSM7438109 E13.5, TdTom-only, replicate 2 E13.5, TdTom-only,
- GSM7438110 E14.5, GFP/TdTom, replicate 1 E14.5, GFP/TdTom,
- GSM7438111 E14.5, GFP/TdTom, replicate 2 E14.5, GFP/TdTom,
- GSM7438112 E14.5, TdTom-only, replicate 1 E14.5, TdTom-only,
- GSM7438113 E14.5, TdTom-only, replicate 2 E14.5, TdTom-only,
- GSM7438114 E16.5, GFP/TdTom, replicate 1 E16.5, GFP/TdTom,
- GSM7438115 E16.5, GFP/TdTom, replicate 2 E16.5, GFP/TdTom,
- GSM7438116 E16.5, TdTom-only, replicate 1 E16.5, TdTom-only,
- GSM7438117 E16.5, TdTom-only, replicate 2 E16.5, TdTom-only,
- GSM7439875 JCB-1 E12.5 GFP+ IgG
- GSM7439876 JCB-2 E12.5 GFP- IgG
- GSM7439877 JCB-4 E12.5 GFP+ GFP
- GSM7439878 JCB-5 E12.5 GFP- GFP
- GSM7439879 JCB-9 E14.5 GFP+ IgG
- GSM7439880 JCB-10 E14.5 GFP- IgG
- GSM7439881 JCB-12 E14.5 GFP+ GFP
- GSM7439882 JCB-13 E14.5 GFP- GFP
- GSE233856 A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain.[RNA-Seq] 24 samples shares atoh1-lineage, developing, decisions, diversity, hindbrain, uncovers, neuronal, neural
- GSE247069 Self-organised pattern formation in the developing dorsal neural tube by a temporal relay of BMP signalling 48 samples shares developing, neural
- GSE63137 Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain 31 samples shares diversity, neuronal
- GSE265784 Cyclin-dependent kinase inhibitors sequentially determine the neural-glial lineage boundaries in the developing cortex 12 samples shares developing, neural
- GSE222950 Krüppel-like factor 4 and 5 oppositely determine neural precursor cell fate in the developing mammalian brain 11 samples shares developing, neural
- GSE319368 Diversity of Cortical Progenitors Directs Neuronal Layer Formation and Regional Glial Patterning 10 samples shares diversity, neuronal
- GSE104323 Transcriptome analysis of single cells from the developing mouse dentate gyrus 232 samples shares developing
- GSE293874 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse bulk RNA-seq] 167 samples shares diversity
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.