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Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1

GSE181019 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2024/03/27 Platform GPL23227
At a glance

Single-cell RNA-seq · human · 16 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
16 samples: 6 conditions, mostly in triplicateGroups 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
Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1Proceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
We explored NGN2’s molecular chromatin function and its ability to induce specific neuronal programs in the context of different cell states and different transcription factor combinations using a series of single cell and bulk genomic sequencing techniques and epigenomic methods.
Published in
Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1
Ang CE, Olmos VH, Vodehnal K et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 38446849 · doi:10.1073/pnas.2308401121
This dataset
Open GSE181019 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 GSE181019_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 PRJNA750423 and SRA study SRP330234. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38446849) ↗
Study design
6 conditions, mostly in triplicate
SLC ×3 SL_Ngn2_2d ×3 SLC_Ngn2_2d ×3 H9_Ngn2_2d ×3 SL ×2 H9 ×2

Supports a between-group comparison across 16 samples.

How we read this: 6 replicated groups read from 16 sample titles; they account for 16 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.