Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A
RNA-seq (gene expression) · human · 11 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
- Homo sapiens (human)
- Samples
- 11 samples: 3 × shControl_Control vs 3 × shKDM2A_Control vs 3 × shControl_Cluster vs 2 × shKDM2A_ClusterGroups 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 GSE316477_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 PRJNA1402981 and SRA study SRP662236. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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.
- GSM9453758 shControl_Control_Rep1 shControl_Control
- GSM9453759 shKDM2A_Control_Rep1 shKDM2A_Control
- GSM9453760 shControl_Cluster_Rep1 shControl_Cluster
- GSM9453761 shControl_Control_Rep2 shControl_Control
- GSM9453762 shKDM2A_Control_Rep2 shKDM2A_Control
- GSM9453763 shControl_Cluster_Rep2 shControl_Cluster
- GSM9453764 shKDM2A_Cluster_Rep2 shKDM2A_Cluster
- GSM9453765 shControl_Control_Rep3 shControl_Control
- GSM9453766 shKDM2A_Control_Rep3 shKDM2A_Control
- GSM9453767 shControl_Cluster_Rep3 shControl_Cluster
- GSM9453768 shKDM2A_Cluster_Rep3 shKDM2A_Cluster
- GSE316752 Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A [ChIP-Seq] 80 samples shares h3k36, kdm2a, demethylase, clustering, metastatic, competence, regulating, enhances
- GSE311698 Structure and mechanism of inhibition of lysine demethylase 2A (KDM2A) by compound 183c 12 samples shares kdm2a, demethylase
- GSE298830 NSD1 governs H3K36me2-mediated DNA methylation and drives differentiation of human iPSCs by regulating lncRNA expression [RNA-seq] 6 samples shares h3k36, regulating
- GSE298831 NSD1 governs H3K36me2-mediated DNA methylation and drives differentiation of human iPSCs by regulating lncRNA expression [ChIP-seq] 8 samples shares h3k36, regulating
- GSE186178 A role for histone lysine demethylase 4 in regulating HBV replication 12 samples shares demethylase, regulating
- GSE279442 SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation [RNA-seq] 50 samples shares h3k36
- GSE276371 Deciphering the interplay between SETD2 mediated H3K36me3 and RNA N6-methyladenosine in clear cell renal cell carcinoma (ccRCC) [RNA-seq] 20 samples shares h3k36
- GSE279619 SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation. 124 samples shares h3k36
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.