The role of the lincRNA Pantr1 during the development of the neurons in the FOXG1 syndrome mouse model
RNA-seq (gene expression) · mouse · 20 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 20 samples: 5 × sh_Pantr1 vs 5 × Sh_Purb vs 5 × Sh_Foxg1 vs 5 × Sh_luciferase(CTL)Groups 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
- The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1Nucleic acids research · 2025
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 GSE172220_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA722484 and SRA study SRP315110. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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.
- GSM5244219 sh_Pantr1 replicate 1 sh_Pantr1
- GSM5244220 sh_Pantr1 replicate 2 sh_Pantr1
- GSM5244221 sh_Pantr1 replicate 3 sh_Pantr1
- GSM5244222 sh_Pantr1 replicate 4 sh_Pantr1
- GSM5244223 sh_Pantr1 replicate 5 sh_Pantr1
- GSM5244224 Sh_Purb replicate 1 Sh_Purb
- GSM5244225 Sh_Purb replicate 2 Sh_Purb
- GSM5244226 Sh_Purb replicate 3 Sh_Purb
- GSM5244227 Sh_Purb replicate 4 Sh_Purb
- GSM5244228 Sh_Purb replicate 5 Sh_Purb
- GSM5244229 Sh_Foxg1 replicate 1 Sh_Foxg1
- GSM5244230 Sh_Foxg1 replicate 2 Sh_Foxg1
- GSM5244231 Sh_Foxg1 replicate 3 Sh_Foxg1
- GSM5244232 Sh_Foxg1 replicate 4 Sh_Foxg1
- GSM5244233 Sh_Foxg1 replicate 5 Sh_Foxg1
- GSM5244234 Sh_luciferase(CTL) replicate 1 Sh_luciferase(CTL)
- GSM5244235 Sh_luciferase(CTL) replicate 2 Sh_luciferase(CTL)
- GSM5244236 Sh_luciferase(CTL) replicate 3 Sh_luciferase(CTL)
- GSM5244237 Sh_luciferase(CTL) replicate 4 Sh_luciferase(CTL)
- GSM5244238 Sh_luciferase(CTL) replicate 5 Sh_luciferase(CTL)
- GSE328896 Patch-seq analysis of dorsal striatum cholinergic interneurons in a mouse model of 22q11 deletion syndrome 125 samples shares neurons
- GSE253919 Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway 15 samples shares foxg1
- GSE84371 Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons 924 samples shares neurons
- GSE274859 Differential neuroprotective and anti-inflammatory effects of dimethyl fumarate, monomethyl fumarate and cannabidiol in neurons and microglia [Mouse] 36 samples shares neurons
- GSE213012 Total and dendritic RNA-sequencing from primary mouse cortical neurons 32 samples shares neurons
- GSE247436 Deletion of Gba in neurons, but not microglia, causes neurodegeneration in a Gaucher mouse model 32 samples shares neurons
- GSE285556 Spatiotemporal Proteomic and Transcriptomic Landscape of DAT+ Dopaminergic Neurons Development and Function 27 samples shares neurons
- GSE191016 Planar cell polarity proteins mediate ketamine-induced restoration of glutamatergic synapses in prefrontal cortical neurons in a mouse model for chronic stress 20 samples shares neurons
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.