PAD4 deletion inhibited obstruction-induced kidney inflammation and fibrosis
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 5 × WT vs 5 × KOGroups 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.
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 GSE272378_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 PRJNA1136535 and SRA study SRP520290. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8399670 WT_1 WT
- GSM8399671 WT_2 WT
- GSM8399672 WT_3 WT
- GSM8399673 WT_4 WT
- GSM8399674 WT_5 WT
- GSM8399675 KO_1 KO
- GSM8399676 KO_2 KO
- GSM8399677 KO_3 KO
- GSM8399678 KO_4 KO
- GSM8399679 KO_5 KO
- GSE330842 GALNT3-deletion suppresses inflammation-associated fibrosis to ameliorates chronic kidney disease via inactivating the TNF-α/NF-kB/MAPK signaling pathway 9 samples shares deletion, fibrosis, kidney
- GSE220322 Gene expression in pre-cystic mouse kidneys after Pkd2 deletion. 48 samples shares deletion, kidney
- GSE284008 RNA-sequencing data from mouse kidneys to identify candidate players in kidneys responding to VNS and/or macrophage-specific deletion of Notch2. 18 samples shares deletion, kidney
- GSE255885 Deletion of Klotho enhancer deepens sexual dimorphism of gene expression without impacting female resistance to kidney injury [RNA exp2] 16 samples shares deletion, kidney
- GSE272105 Bulk RNAseq analysis of Cx3cr1+ macrophages with and without IL4Ra deletion during bleomycin-induced lung fibrosis. 12 samples shares deletion, fibrosis
- GSE226120 Effect of TSPO deletion within mouse hippocampus under neuroinflammation 16 samples shares deletion
- GSE271317 Deletion of Bmal1 in Intestinal Epithelium Protects against Colonic Inflammation by Suppressing the Apoptosis Pathway 12 samples shares deletion
- GSE305276 Osteocyte-specific deletion of Gasdermin D drives osteoarthritis cartilage degeneration by promoting inflammation and remodeling in subchondral bone 9 samples shares deletion
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.