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Decoding Transcriptional Identity in Developing Human Sensory Neurons and Organoid Modeling

GSE245310 Homo sapiens (human) Single-cell RNA-seq 68 samples Submitted 2024/09/05 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 68 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
68 samples: 11 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.
Paper
Decoding transcriptional identity in developing human sensory neurons and organoid modelingCell · 2024
Summary (written by the submitters)
Dorsal root ganglia (DRG) play a crucial role in processing sensory information, making it essential to understand their development. Here, we construct a single-cell spatiotemporal transcriptomic atlas of human embryonic DRG. This atlas reveals the diversity of cell types and highlights the extrinsic signaling cascades and intrinsic regulatory hierarchies that guide cell fate decisions, including neuronal/glial lineage restriction, sensory neuron differentiation and specification, and the formation of neuron-satellite glial cell (SGC) unit.
Read the full summary ↓
Additionally, we identify a human-enriched NTRK3+/DCC+ nociceptor subtype, which is involved in multimodal nociceptive processing. Mimicking the programmed activation of signaling pathways in vivo, we successfully establish functional human DRG organoids and underscore the critical roles of transcriptional regulators in the fate commitment of unspecialized sensory neurons (uSNs). Overall, our research elucidates the multilevel signaling pathways and transcription factor (TF) regulatory hierarchies that underpin the diversity of somatosensory neurons, emphasizing the phenotypic distinctions in human nociceptor subtypes.
Published in
Decoding transcriptional identity in developing human sensory neurons and organoid modeling
Lu T, Wang M, Zhou W et al. · Cell 2024 · PMID 39536745 · doi:10.1016/j.cell.2024.10.023
This dataset
Open GSE245310 in finder → Find more human 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 GSE245310_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 PRJNA1027805 and SRA study SRP466253. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39536745) ↗
Study design
11 conditions, mostly with about 4 replicates each
DRG_GW8_sample1_lane1_S2 ×4 DRG_GW8_sample1_lane2_S2 ×4 DRG_GW8_sample1_lane3-S2 ×4 DRG_GW7_sample2_lane1_S1 ×4 DRG_GW7_sample2_lane2_S1 ×4 DRG_GW7_sample2_lane3_S1 ×4 DRG8_GW14_S1_L001_R1 ×4 DRG9_GW17_S1_L001_R1 ×4 +27 more

Supports a between-group comparison across 44 samples.

How we read this: 11 replicated groups read from 68 sample titles; they account for 44 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

+ 28 more — browse all 68 samples with per-sample file links →

Datasets on a similar topic

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