RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [RNA-Seq]
RNA-seq (gene expression) · human · 28 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
- 28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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
- RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcriptionbioRxiv : the preprint server for biology · 2025
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 GSE300418_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 PRJNA1280910 and SRA study SRP594051. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 28 sample titles: 28 distinct titles with little repetition. 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.
- GSM9060212 LSK cells, ENL-WT, replicate1, RNA-seq
- GSM9060213 LSK cells, ENL-WT, replicate2, RNA-seq
- GSM9060214 LSK cells, ENL-T1, replicate1, RNA-seq
- GSM9060215 LSK cells, ENL-T1, replicate2, RNA-seq
- GSM9060216 LSK cells, ENL-T1-3A, replicate1, RNA-seq
- GSM9060217 LSK cells, ENL-T1-3A, replicate2, RNA-seq
- GSM9060218 MDA231 cells, ENL-WT, replicate1, RNA-seq
- GSM9060219 MDA231 cells, ENL-WT, replicate2, RNA-seq
- GSM9060220 MDA231 cells, ENL-T1, replicate1, RNA-seq
- GSM9060221 MDA231 cells, ENL-T1, replicate2, RNA-seq
- GSM9060222 MDA231 cells, ENL-T1-3A, replicate1, RNA-seq
- GSM9060223 MDA231 cells, ENL-T1-3A, replicate2, RNA-seq
- GSM9060224 MDA231 cells, ENL-T2, replicate1, RNA-seq
- GSM9060225 MDA231 cells, ENL-T2, replicate2, RNA-seq
- GSM9060226 MDA231 cells, ENL-T2-3A, replicate1, RNA-seq
- GSM9060227 MDA231 cells, ENL-T2-3A, replicate2, RNA-seq
- GSM9060228 HEK293 cells, ENL-WT, replicate1, RNA-seq
- GSM9060229 HEK293 cells, ENL-WT, replicate2, RNA-seq
- GSM9060230 HEK293 cells, ENL-T2, replicate1, RNA-seq
- GSM9060231 HEK293 cells, ENL-T2, replicate2, RNA-seq
- GSM9060232 HEK293 cells, ENL-T2-3A, replicate1, RNA-seq
- GSM9060233 HEK293 cells, ENL-T2-3A, replicate2, RNA-seq
- GSM9060234 HEK293 cells, ENL-WT, replicate3, RNA-seq
- GSM9060235 HEK293 cells, ENL-WT, replicate4, RNA-seq
- GSM9060236 HEK293 cells, ENL-T1, replicate1, RNA-seq
- GSM9060237 HEK293 cells, ENL-T1, replicate2, RNA-seq
- GSM9060238 HEK293 cells, ENL-T1-3A, replicate1, RNA-seq
- GSM9060239 HEK293 cells, ENL-T1-3A, replicate2, RNA-seq
- GSE297591 Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [RNA-seq] 96 samples shares chromatin-associated, rna-seq
- GSE294247 The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing 110 samples shares oncogenic
- GSE274098 Recurrent FGFR-alterations are frequent oncogenic drivers and therapeutic targets in pediatric low-grade gliomas 68 samples shares oncogenic
- GSE315010 Abrogation of Oncogenic RAS Signaling by a RAS(ON) Inhibitor Doublet Primes Immune-refractory KRASG12C-mutant NSCLC for Immune Checkpoint Blockade 44 samples shares oncogenic
- GSE302363 Selective RNA sequestration in biomolecular condensates directs cell fate transitions 40 samples shares condensates
- GSE312638 Catestatin impedes melanoma progression and drug resistance by reprogramming oncogenic signaling pathways 22 samples shares oncogenic
- GSE241347 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates leukemogenesis 291 samples shares chromatin-associated
- GSE155631 Oncogenic mechanisms of DIS3 mutations in Multiple Myeloma 62 samples shares oncogenic
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.