Single Cell Chromatin Accessibility Profiling on the mouse kidneys with ischemia-reperfusion injury
Single-cell RNA-seq · mouse · 19 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 19 samples: 6 conditions, mostly in triplicateGroups 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
- Epigenetic reprogramming driving successful and failed repair in acute kidney injuryScience advances · 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 GSE252105_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1057807 and SRA study SRP480325. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 6 replicated groups read from 19 sample titles; they account for 19 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.
- GSM7993677 14day-1 14day
- GSM7993678 2day-1 2day
- GSM7993679 2day-2 2day
- GSM7993680 sham-1 sham
- GSM7993681 14day-2 14day
- GSM7993682 14day-3 14day
- GSM7993683 sham-2 sham
- GSM7993684 4hr-1 4h
- GSM7993685 4hr-2 4h
- GSM7993686 42day-1 42day
- GSM7993687 2day-3 2day
- GSM7993688 12hr-1 12h
- GSM7993689 12hr-2 12h
- GSM7993690 12hr-3 12h
- GSM7993691 4hr-3 4h
- GSM7993692 4hr-4 4h
- GSM7993693 sham-3 sham
- GSM7993694 42day-2 42day
- GSM7993695 42day-3 42day
- GSE274819 Single-cell RNA sequencing of murine kidneys for ischemia-reperfusion induced renal injury and fibrosis 10 samples shares ischemia-reperfusion, kidneys, injury
- GSE216371 A single-cell atlas of chromatin accessibility in mouse organogenesis 68 samples shares accessibility, chromatin
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares accessibility, chromatin
- GSE249077 Mapping the female mouse chromatin accessibility landscape by UUATAC-seq 23 samples shares accessibility, chromatin
- GSE342565 Chromatin accessibility profiling of high endothelial cells (HECs) from mouse peripheral lymph node and Peyer's patch by ATAC-seq 2 samples shares accessibility, chromatin
- GSE266022 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq] 24 samples shares chromatin, injury
- GSE246986 Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement 24 samples shares accessibility, chromatin
- GSE309545 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [multiome mouse] 64 samples shares accessibility, chromatin
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.