Transcriptomic analysis of the spinal cords of knock-in adult mice carrying the ATXN2/TDP-43 human transgenes
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 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
- ATAXIN-2 intermediate-length polyglutamine expansions elicit ALS-associated metabolic and immune phenotypesNature communications · 2024
Read the full summary ↓
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 GSE224580_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 PRJNA934448 and SRA study SRP424177. 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 18 sample titles: 18 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.
- GSM7026636 Spinal cord, NTg animal (1212)
- GSM7026637 Spinal cord, NTg animal (1217)
- GSM7026638 Spinal cord, NTg animal (1226)
- GSM7026639 Spinal cord, Q22 animal (4712)
- GSM7026640 Spinal cord, Q22 animal (5079)
- GSM7026641 Spinal cord, Q22 animal (5178)
- GSM7026642 Spinal cord, Q33 animal (8610)
- GSM7026643 Spinal cord, Q33 animal (8620)
- GSM7026644 Spinal cord, Q33 animal (8695)
- GSM7026645 Spinal cord, TDP-43 animal (8859)
- GSM7026646 Spinal cord, TDP-43 animal (9285)
- GSM7026647 Spinal cord, TDP-43 animal (9413)
- GSM7026648 Spinal cord, Q22;TDP-43 animal (4221)
- GSM7026649 Spinal cord, Q22;TDP-43 animal (4230)
- GSM7026650 Spinal cord, Q22;TDP-43 animal (4307)
- GSM7026651 Spinal cord, Q33;TDP-43 animal (4539)
- GSM7026652 Spinal cord, Q33;TDP-43 animal (4577)
- GSM7026653 Spinal cord, Q33;TDP-43 animal (4578)
- GSE224581 Transcriptomic analysis of spinal cord microglial cells from NTg and ATXN2-Q33;TDP-43 adult mice 6 samples shares tdp-43, atxn2, spinal, adult
- GSE297399 Viral-mediated knockdown of Atxn2 attenuates TDP-43 pathology and muscle dysfunction in the PFN1C71G ALS mouse model 52 samples shares tdp-43, atxn2
- GSE287573 TMEM106B deficiency leads to alterations in lipid metabolism and obesity in the TDP-43Q331K knock-in mouse model 37 samples shares tdp-43, knock-in
- GSE283631 Transcriptomic analysis of miAtxn2 knockdown effects on lumbar spinal cord in the TAR4/4 sporadic ALS mouse model 16 samples shares atxn2, spinal
- GSE328214 Single-cell analysis of mouse microglia carrying the mouse Nlrp3 wildtype locus, the human NLRP3 wildtype knock-in or the human NLRP3 D305N variant knock-in gene. 8 samples shares knock-in, carrying
- GSE267069 A fluorescent perilipin 2 knock-in mouse model reveals a high abundance of lipid droplets in the developing and adult brain 2 samples shares knock-in, adult
- GSE288185 TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability 86 samples shares tdp-43
- GSE300423 LINE-1 retrotransposition in a mouse TDP-43 model of neurodegeneration marks motor cortex neurons for cell-intrinsic and cell non-autonomous programmed cell death. 45 samples shares tdp-43
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.