CSMD3 loss drives aggressive behavior and tumor consolidation in oral squamous premalignant cells
RNA-seq (gene expression) · mouse · 9 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
- 9 samples: 3 × CSMD3, KO guide 1, vs 3 × CSMD3, KO guide 2, vs 3 × WT Control,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.
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 GSE342871_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 PRJNA1508999 and SRA study SRP725015. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM9941252 CSMD3, KO guide 1, rep 1 CSMD3, KO guide 1,
- GSM9941253 CSMD3, KO guide 1, rep 2 CSMD3, KO guide 1,
- GSM9941254 CSMD3, KO guide 1, rep 3 CSMD3, KO guide 1,
- GSM9941255 CSMD3, KO guide 2, rep 1 CSMD3, KO guide 2,
- GSM9941256 CSMD3, KO guide 2, rep 2 CSMD3, KO guide 2,
- GSM9941257 CSMD3, KO guide 2, rep 3 CSMD3, KO guide 2,
- GSM9941258 WT Control, rep 1 WT Control,
- GSM9941259 WT Control, rep 2 WT Control,
- GSM9941260 WT Control, rep 3 WT Control,
- GSE305085 Oncogenic Ras drives EED degradation and PRC2 dysfunction to promote aggressive squamous cell carcinoma [mouse RNA-Seq] 6 samples shares aggressive, squamous, drives
- GSE305084 Oncogenic Ras drives EED degradation and PRC2 dysfunction to promote aggressive squamous cell carcinoma [mouse CUT & RUN] 12 samples shares aggressive, squamous, drives
- GSE287166 Molecular Features of Aggressive Preinvasive Lesions driven by Combined MYC Activation and PTEN Loss in Mouse Prostate 21 samples shares aggressive, loss
- GSE305505 Genitourinary defects, anxiety and aggressive-like behavior and glucose metabolism disorders in Zmym2 mutant mice with inserted piggyBac transposon 9 samples shares aggressive, behavior
- GSE278530 JAK inhibition results in aggressive cutaneous squamous cell carcinoma through MAPK pathway activation and shapes the tumor immune microenvironment to create novel therapeutic opportunities [RNA-seq] 7 samples shares aggressive, squamous
- GSE273079 Castration Increases Aggressiveness of Prostatic Luminal Progenitor Cells in Prostate Cancer Through FosL1/AP-1-Mediated Transcriptional Reprogramming 384 samples shares aggressive
- GSE278570 Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressiveness 309 samples shares aggressive
- GSE300675 Neuron type-specific mRNA translation programs provide a gateway for memory consolidation. 153 samples shares consolidation
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.