Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion
Single-cell RNA-seq · mouse · 13 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
- Mus musculus (mouse)
- Samples
- 13 samples: 13 samples, each with a distinct title — no replicated groupsGroups 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
- Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansionNature communications · 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 GSE229129_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 PRJNA953007 and SRA study SRP431357. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 13 sample titles: 13 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.
- GSM7153007 12-5-1_E12.5 Control
- GSM7153008 12-5-3_E12.5 BRN1/2 cKO
- GSM7153009 14-5-2_E14.5 Control
- GSM7153010 14-5-5_E14.5 BRN1/2 cKO
- GSM7153011 C1_E14.5 BRN1/2 cKO
- GSM7153012 C5_E14.5 Control
- GSM7153013 C6_E14.5 Control
- GSM7153014 D3_E12.5 Control
- GSM7153015 D5_E12.5 BRN1/2 cKO
- GSM7153016 E2_E12.5 Control
- GSM7153017 E6_E12.5 BRN1/2 cKO
- GSM7153018 4220_E14.5 BRN1/2 cKO
- GSM7153019 4850_E14.5 BRN1/2 cKO
- GSE291075 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - ex vivo, Nfil3] 27 samples shares specification, progenitors
- GSE293151 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm. 24 samples shares specification, mammalian
- GSE291316 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - Tox] 12 samples shares specification, progenitors
- GSE291076 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - Il7rLT] 12 samples shares specification, progenitors
- GSE291317 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [scRNA-seq] 6 samples shares specification, progenitors
- GSE254428 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq] 2 samples shares specification, mammalian
- GSE291077 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors 70 samples shares specification, progenitors
- GSE294521 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG] 34 samples shares specification, mammalian
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.