Progranulin insufficiency and TDP-43 overexpression interact to worsen FTD-related phenotypes in mice.
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 6 × Het_Neg vs 6 × WT_Neg vs 6 × WT_Pos vs 6 × Het_PosGroups 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.
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 GSE305500_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 PRJNA1306103 and SRA study SRP608970. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 4 replicated groups read from 24 sample titles; they account for 24 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.
- GSM9178123 Het_Neg441 Het_Neg
- GSM9178124 Het_Neg448 Het_Neg
- GSM9178125 WT_Neg455 WT_Neg
- GSM9178126 WT_Pos460 WT_Pos
- GSM9178127 Het_Pos461 Het_Pos
- GSM9178128 WT_Neg463 WT_Neg
- GSM9178129 Het_Pos465 Het_Pos
- GSM9178130 Het_Pos467 Het_Pos
- GSM9178131 WT_Pos470 WT_Pos
- GSM9178132 WT_Pos471 WT_Pos
- GSM9178133 Het_Pos474 Het_Pos
- GSM9178134 WT_Neg476 WT_Neg
- GSM9178135 WT_Pos478 WT_Pos
- GSM9178136 WT_Neg481 WT_Neg
- GSM9178137 WT_Pos487 WT_Pos
- GSM9178138 Het_Pos490 Het_Pos
- GSM9178139 WT_Neg493 WT_Neg
- GSM9178140 WT_Neg496 WT_Neg
- GSM9178141 Het_Neg497 Het_Neg
- GSM9178142 WT_Pos498 WT_Pos
- GSM9178143 Het_Pos500 Het_Pos
- GSM9178144 Het_Neg503 Het_Neg
- GSM9178145 Het_Neg511 Het_Neg
- GSM9178146 Het_Neg514 Het_Neg
- GSE283998 MBNL overexpression rescues cardiac phenotypes in a myotonic dystrophy type 1 heart mouse model 36 samples shares overexpression, phenotypes
- GSE262341 Multi-omics analysis of sarcospan overexpression in mdx skeletal muscle reveals compensatory remodeling of cytoskeleton-matrix interactions that promote mechanotransduction pathways 13 samples shares overexpression, interact
- GSE288185 TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability 86 samples shares tdp-43
- GSE297399 Viral-mediated knockdown of Atxn2 attenuates TDP-43 pathology and muscle dysfunction in the PFN1C71G ALS mouse model 52 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
- GSE287573 TMEM106B deficiency leads to alterations in lipid metabolism and obesity in the TDP-43Q331K knock-in mouse model 37 samples shares tdp-43
- GSE27218 Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq) 21 samples shares tdp-43
- GSE224580 Transcriptomic analysis of the spinal cords of knock-in adult mice carrying the ATXN2/TDP-43 human transgenes 18 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.