Transcriptomic analysis of HIV-associated nephropathy (Tg26) mouse kidney
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: 20 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
- PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathyeLife · 2024
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 GSE205060_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 PRJNA843463 and SRA study SRP377561. 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 20 sample titles: 20 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.
- GSM6204647 41_Ctrl_WT_1
- GSM6204648 42_Ctrl_WT_2
- GSM6204649 43_Ctrl_WT_3
- GSM6204650 44_Ctrl_Tg_1
- GSM6204651 45_Ctrl_Tg_2
- GSM6204652 46_Ctrl_Tg_3
- GSM6204653 47_C16_WT_1
- GSM6204654 48_C16_WT_2
- GSM6204655 49_C16_WT_3
- GSM6204656 50_C16_Tg_1
- GSM6204657 51_C16_Tg_2
- GSM6204658 52_C16_Tg_3
- GSM6204659 1_WT
- GSM6204660 2_Tg26
- GSM6204661 3_Tg26_C16
- GSM6204662 4_Tg26_Glom
- GSM7401905 5_WT_B
- GSM7401906 6_Tg26_B
- GSM7401907 7_Tg26_C16_B
- GSM7401908 8_Glom_WT
- GSE227234 Transcriptomic analysis of transgenic mouse kidney glomeruli with HIV-associated nephropathy (Tg26) and human APOL1 variants expression [bulk RNA-seq] 34 samples shares tg26, hiv-associated, nephropathy, kidney
- GSE205058 Transcriptomic analysis of HIV-associated nephropathy (Tg26) mouse kidney [bulk RNA-seq] 12 samples shares tg26, hiv-associated, nephropathy, kidney
- GSE282711 Cross-Species Comparison between Mouse Kidney Multi-Omics and Human Genome-Wide Association Studies Highlights Molecular Features Associated with Oxalate Nephropathy 12 samples shares nephropathy, kidney
- GSE317491 Kidney Transcriptome Sequencing of Mice with Diabetic Nephropathy 6 samples shares nephropathy, kidney
- GSE192687 Single-cell RNAseq analysis of renal endothelial cells in murine diabetic nephropathy 5464 samples shares nephropathy
- GSE205592 Obesity-instructed TREM2-high macrophages identified by comparative analysis of diabetic mouse and human kidney at single-cell resolution [scRNA-seq: DKD_mouse] 41 samples shares kidney
- GSE289432 Y665F variant of mouse STAT5b protects against acute kidney injury through transcriptomic shifts in renal gene expression 32 samples shares kidney
- GSE205593 Obesity-instructed TREM2-high macrophages identified by comparative analysis of diabetic mouse and human kidney at single-cell resolution [scRNA-seq: Baseline_mouse] 24 samples shares kidney
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.