A disease similarity approach identifies short-lived Niemann-Pick type C disease mice with accelerated brain aging as a novel mouse model for Alzheimer’s disease and aging research
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × wildtype male mice FC vs 3 × wildtype female mice FC vs 3 × NPC1KO male mice FC vs 3 × NPC1KO female mice FCGroups 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
- A disease similarity approach identifies short-lived Niemann-Pick type C disease mice with accelerated brain aging as a novel mouse model for Alzheimer's disease and aging researchbioRxiv : the preprint server for biology · 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 GSE266485_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 PRJNA1107268 and SRA study SRP505439. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8248001 wildtype male mice FC 1 wildtype male mice FC
- GSM8248002 wildtype male mice FC 2 wildtype male mice FC
- GSM8248003 wildtype male mice FC 3 wildtype male mice FC
- GSM8248004 wildtype female mice FC 1 wildtype female mice FC
- GSM8248005 wildtype female mice FC 2 wildtype female mice FC
- GSM8248006 wildtype female mice FC 3 wildtype female mice FC
- GSM8248007 NPC1KO male mice FC 1 NPC1KO male mice FC
- GSM8248008 NPC1KO male mice FC 2 NPC1KO male mice FC
- GSM8248009 NPC1KO male mice FC 3 NPC1KO male mice FC
- GSM8248010 NPC1KO female mice FC 1 NPC1KO female mice FC
- GSM8248011 NPC1KO female mice FC 2 NPC1KO female mice FC
- GSM8248012 NPC1KO female mice FC 3 NPC1KO female mice FC
- GSE282066 Accelerated Midlife Endocrine and Bioenergetic Brain Aging in APOE4 Female Mice 59 samples shares accelerated, brain
- GSE242502 Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus [midbrain] 10 samples shares accelerated, brain
- GSE325488 Accelerated cerebromicrovascular senescence contributes to cognitive decline in a mouse model of paclitaxel (Taxol)-induced chemobrain 8 samples shares accelerated, brain
- GSE116071 Human forebrain expansion is regulated by a human accelerated region controlling early Foxg1 expression 2 samples shares accelerated, brain
- GSE307881 Mouse Offspring Conceived by In Vitro Fertilization Exhibit Accelerated Reproductive Aging Through Early Ovarian Failure 151 samples shares accelerated
- GSE330229 Accelerated RNA polymerase II elongation drives endothelial transition and plaque vulnerability: pharmacological targeting of the super elongation complex [RNA-seq] 24 samples shares accelerated
- GSE242504 Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus 20 samples shares accelerated
- GSE250438 Role of the TRIF-IFN-I pathway in Helicobacter-induced gastric cancer progression in an accelerated murine disease model 19 samples shares accelerated
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.