A chronic, low-dose treatment with methamphetamine modulates genes implicated in neurodegeneration in a transgenic model of NeuroHIV
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: 24 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
- Chronic, Low-Dose Methamphetamine Reveals Sexual Dimorphism of Memory Performance, Histopathology, and Gene Expression Affected by HIV-1 Tat Protein in a Transgenic Model of NeuroHIVViruses · 2025
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 GSE255016_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 PRJNA1073205 and SRA study SRP488024. 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 24 sample titles: 24 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.
- GSM8062597 Ctl 1, Male
- GSM8062598 Ctl 2, Male
- GSM8062599 Ctl 3, Male
- GSM8062600 Ctl 4, Female
- GSM8062601 Ctl 5, Female
- GSM8062602 Ctl 6, Female
- GSM8062603 Tat 1, Male
- GSM8062604 Tat 2, Male
- GSM8062605 Tat 3, Male
- GSM8062606 Tat 4, Female
- GSM8062607 Tat 5, Female
- GSM8062608 Tat 6, Female
- GSM8062609 METH 1, Male
- GSM8062610 METH 2, Male
- GSM8062611 METH 3, Male
- GSM8062612 METH 4, Female
- GSM8062613 METH 5, Female
- GSM8062614 METH 6, Female
- GSM8062615 Tat+METH 1, Male
- GSM8062616 Tat+METH 2, Male
- GSM8062617 Tat+METH 3, Male
- GSM8062618 Tat+METH 4, Female
- GSM8062619 Tat+METH 5, Female
- GSM8062620 Tat+METH 6, Female
- GSE103334 Temporal tracking of microglia activation in neurodegeneration at single-cell resolution 2208 samples shares neurodegeneration
- GSE254996 ACSS2 upregulation enhances neuronal resilience to aging and neurodegeneration [RNA-seq] 98 samples shares neurodegeneration
- GSE255633 Region-specific pathogenesis and dissipation of intraregional heterogeneity in cerebellar neurodegeneration 49 samples shares neurodegeneration
- GSE309471 Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis 46 samples shares transgenic
- 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 neurodegeneration
- GSE297457 A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration 44 samples shares neurodegeneration
- GSE43366 Defining the microglia transcriptome during disease progression in ALS transgenic mice 42 samples shares transgenic
- GSE281823 Transcriptional profiling of striatum from the Q140 mouse model of Huntington's disease, from A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy 40 samples shares neurodegeneration
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.