Bulk RNA-Seq from kidneys of uninephrectomized db/db mice as a model of severe diabetic kidney disease
RNA-seq (gene expression) · mouse · 28 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
- 28 samples: 12 × db/db, 26w, vs 6 × db/m, 35w, vs 5 × db/m, 26w, vs 5 × db/db, 35w,Groups 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
- Renal transcriptome analysis of uninephrectomized db/db mice identified a mechanism for the transition to severe diabetic nephropathyExperimental animals · 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 GSE228960_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 PRJNA952248 and SRA study SRP430882. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 28 samples.
How we read this: 4 replicated groups read from 28 sample titles; they account for 28 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.
- GSM7146220 db/m, 26w, 01 db/m, 26w,
- GSM7146221 db/m, 26w, 02 db/m, 26w,
- GSM7146222 db/m, 26w, 03 db/m, 26w,
- GSM7146223 db/m, 26w, 04 db/m, 26w,
- GSM7146224 db/m, 26w, 05 db/m, 26w,
- GSM7146225 db/db, 26w, 01 db/db, 26w,
- GSM7146226 db/db, 26w, 02 db/db, 26w,
- GSM7146227 db/db, 26w, 03 db/db, 26w,
- GSM7146228 db/db, 26w, 04 db/db, 26w,
- GSM7146229 db/db, 26w, 05 db/db, 26w,
- GSM7146230 db/db, 26w, 06 db/db, 26w,
- GSM7146231 db/db, 26w, 07 db/db, 26w,
- GSM7146232 db/db, 26w, 08 db/db, 26w,
- GSM7146233 db/db, 26w, 09 db/db, 26w,
- GSM7146234 db/db, 26w, 10 db/db, 26w,
- GSM7146235 db/db, 26w, 11 db/db, 26w,
- GSM7146236 db/db, 26w, 12 db/db, 26w,
- GSM7146237 db/m, 35w, 01 db/m, 35w,
- GSM7146238 db/m, 35w, 02 db/m, 35w,
- GSM7146239 db/m, 35w, 03 db/m, 35w,
- GSM7146240 db/m, 35w, 04 db/m, 35w,
- GSM7146241 db/m, 35w, 05 db/m, 35w,
- GSM7146242 db/m, 35w, 06 db/m, 35w,
- GSM7146243 db/db, 35w, 01 db/db, 35w,
- GSM7146244 db/db, 35w, 02 db/db, 35w,
- GSM7146245 db/db, 35w, 03 db/db, 35w,
- GSM7146246 db/db, 35w, 05 db/db, 35w,
- GSM7146247 db/db, 35w, 06 db/db, 35w,
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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.