Vhl and Rassf1a mutations cause DNA damage, chromosomal instability and induce gene expression changes characteristic of ccRCC [scRNA-seq]
Single-cell RNA-seq · mouse · 16 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
- 16 samples: 4 × WT vs 4 × Vhl vs 4 × Rassf1a vs 4 × Vhl/Rassf1aGroups 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.
Read the full summary ↓
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 GSE280281_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 PRJNA1177518 and SRA study SRP540722. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM8593988 WT rep1 WT
- GSM8593989 WT rep2 WT
- GSM8593990 WT rep3 WT
- GSM8593991 WT rep4 WT
- GSM8593992 Vhl rep1 Vhl
- GSM8593993 Vhl rep2 Vhl
- GSM8593994 Vhl rep3 Vhl
- GSM8593995 Vhl rep4 Vhl
- GSM8593996 Rassf1a rep1 Rassf1a
- GSM8593997 Rassf1a rep2 Rassf1a
- GSM8593998 Rassf1a rep3 Rassf1a
- GSM8593999 Rassf1a rep4 Rassf1a
- GSM8594000 Vhl/Rassf1a rep1 Vhl/Rassf1a
- GSM8594001 Vhl/Rassf1a rep2 Vhl/Rassf1a
- GSM8594002 Vhl/Rassf1a rep3 Vhl/Rassf1a
- GSM8594003 Vhl/Rassf1a rep4 Vhl/Rassf1a
- GSE280300 Vhl and Rassf1a mutations cause DNA damage, chromosomal instability and induce gene expression changes characteristic of ccRCC [bulk RNA-seq] 24 samples shares rassf1a, characteristic, chromosomal, instability, mutations, changes, damage
- GSE261555 Chromosomal instability can favor macrophage-mediated immune response and induce a broad, vaccination-like anti-tumor IgG response [scRNA-Seq] 2 samples shares chromosomal, instability, scrna-seq
- GSE234031 Telomeric Chromosomal Instability Fosters Paracrine Mediated Cell Competition to Initiate Intestinal Cancer [scRNA-seq] 2 samples shares chromosomal, instability, scrna-seq
- GSE252120 Oxidative stress induced telomere instability/damage drives T cell dysfunction in cancer 32 samples shares instability, damage
- GSE254325 Epigenetic regulation of chromosomal instability by EZH2 methyltransferase [RNA-seq] 12 samples shares chromosomal, instability
- GSE217457 scRNA-seq analysis revealed the molecular characteristics of HSPCs and erythroid cells in bone marrow upon HAPC 10 samples shares characteristic, scrna-seq
- GSE261556 Chromosomal instability can favor macrophage-mediated immune response and induce a broad, vaccination-like anti-tumor IgG response [RNA-Seq] 6 samples shares chromosomal, instability
- GSE216683 scRNA-seq analysis revealed the molecular characteristics of erythroid cells in spleen upon HAPC 4 samples shares characteristic, scrna-seq
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.