Transcriptomic analysis of HIV-associated nephropathy (Tg26) mouse kidney [bulk RNA-seq]
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: 12 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 GSE205058_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 PRJNA843467 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 12 sample titles: 12 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
- GSE228960 Bulk RNA-Seq from kidneys of uninephrectomized db/db mice as a model of severe diabetic kidney disease 28 samples shares rna-seq, kidney, bulk
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq, bulk
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq, bulk
- GSE271662 RNA-seq of Mouse Spinal Cord after Lateral Compression Spinal Cord Injury followed by Delayed Atorvastatin or Vehicle Treatment [Bulk RNA-seq of mice spinal cords] 16 samples shares rna-seq, bulk
- GSE220675 Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI [scRNA-seq] 11 samples shares rna-seq, kidney
- GSE317491 Kidney Transcriptome Sequencing of Mice with Diabetic Nephropathy 6 samples shares nephropathy, kidney
- GSE292377 Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq] 41 samples shares rna-seq, bulk
- GSE192687 Single-cell RNAseq analysis of renal endothelial cells in murine diabetic nephropathy 5464 samples shares nephropathy
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.