Vhl and Rassf1a mutations cause DNA damage, chromosomal instability and induce gene expression changes characteristic of ccRCC [bulk RNA-seq]
Single-cell RNA-seq · mouse · 24 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 24 samples: 8 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.
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 GSE280300_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 PRJNA1177786 and SRA study SRP540814. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM8594414 WT GFP rep1 WT GFP
- GSM8594415 WT GFP rep2 WT GFP
- GSM8594416 WT GFP rep3 WT GFP
- GSM8594417 WT Cre rep1 WT Cre
- GSM8594418 WT Cre rep2 WT Cre
- GSM8594419 WT Cre rep3 WT Cre
- GSM8594420 Vhl GFP rep1 Vhl GFP
- GSM8594421 Vhl GFP rep2 Vhl GFP
- GSM8594422 Vhl GFP rep3 Vhl GFP
- GSM8594423 Vhl Cre rep1 Vhl Cre
- GSM8594424 Vhl Cre rep2 Vhl Cre
- GSM8594425 Vhl Cre rep3 Vhl Cre
- GSM8594426 Rassf1a GFP rep1 Rassf1a GFP
- GSM8594427 Rassf1a GFP rep2 Rassf1a GFP
- GSM8594428 Rassf1a GFP rep3 Rassf1a GFP
- GSM8594429 Rassf1a Cre rep1 Rassf1a Cre
- GSM8594430 Rassf1a Cre rep2 Rassf1a Cre
- GSM8594431 Rassf1a Cre rep3 Rassf1a Cre
- GSM8594432 Vhl/Rassf1a GFP rep1 Vhl/Rassf1a GFP
- GSM8594433 Vhl/Rassf1a GFP rep2 Vhl/Rassf1a GFP
- GSM8594434 Vhl/Rassf1a GFP rep3 Vhl/Rassf1a GFP
- GSM8594435 Vhl/Rassf1a Cre rep1 Vhl/Rassf1a Cre
- GSM8594436 Vhl/Rassf1a Cre rep2 Vhl/Rassf1a Cre
- GSM8594437 Vhl/Rassf1a Cre rep3 Vhl/Rassf1a Cre
- GSE280281 Vhl and Rassf1a mutations cause DNA damage, chromosomal instability and induce gene expression changes characteristic of ccRCC [scRNA-seq] 16 samples shares rassf1a, characteristic, chromosomal, instability, mutations, changes, rna-seq, damage
- GSE254325 Epigenetic regulation of chromosomal instability by EZH2 methyltransferase [RNA-seq] 12 samples shares chromosomal, instability, rna-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, rna-seq
- GSE234032 Telomeric Chromosomal Instability Fosters Paracrine Mediated Cell Competition to Initiate Intestinal Cancer [bulk RNA-seq] 4 samples shares chromosomal, instability, rna-seq
- 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, rna-seq
- GSE234031 Telomeric Chromosomal Instability Fosters Paracrine Mediated Cell Competition to Initiate Intestinal Cancer [scRNA-seq] 2 samples shares chromosomal, instability, rna-seq
- GSE326003 The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence [RNA-seq] 165 samples shares characteristic, rna-seq
- GSE252120 Oxidative stress induced telomere instability/damage drives T cell dysfunction in cancer 32 samples shares instability, damage
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.