Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes [RNA-Seq]
RNA-seq (gene expression) · human · 99 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
- 99 samples: 32 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.
- Paper
- Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymesCommunications 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 GSE254242_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 PRJNA1069072 and SRA study SRP485989. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 99 samples.
How we read this: 32 replicated groups read from 99 sample titles; they account for 99 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.
- GSM8036431 GP5d, DNMTi Rep1 GP5d, DNMTi
- GSM8036432 GP5d, DNMTi Rep2 GP5d, DNMTi
- GSM8036433 GP5d, DNMTi Rep3 GP5d, DNMTi
- GSM8036434 GP5d, HDACi Rep1 GP5d, HDACi
- GSM8036435 GP5d, HDACi Rep2 GP5d, HDACi
- GSM8036436 GP5d, HDACi Rep3 GP5d, HDACi
- GSM8036437 GP5d, SETDB1i Rep1 GP5d, SETDB1i
- GSM8036438 GP5d, SETDB1i Rep2 GP5d, SETDB1i
- GSM8036439 GP5d, SETDB1i Rep3 GP5d, SETDB1i
- GSM8036440 OE19, DMSO Rep1 OE19, DMSO
- GSM8036441 OE19, DMSO Rep2 OE19, DMSO
- GSM8036442 OE19, DMSO Rep3 OE19, DMSO
- GSM8036443 OE19, DNMTi Rep1 OE19, DNMTi
- GSM8036444 OE19, DNMTi Rep2 OE19, DNMTi
- GSM8036445 OE19, DNMTi Rep3 OE19, DNMTi
- GSM8036446 OE19, HDACi Rep1 OE19, HDACi
- GSM8036447 OE19, HDACi Rep2 OE19, HDACi
- GSM8036448 OE19, HDACi Rep3 OE19, HDACi
- GSM8036449 OE19, SETDB1i Rep1 OE19, SETDB1i
- GSM8036450 OE19, SETDB1i Rep2 OE19, SETDB1i
- GSM8036451 OE19, SETDB1i Rep3 OE19, SETDB1i
- GSM8036452 OE19, DNMTi-HDACi Rep1 OE19, DNMTi-HDACi
- GSM8036453 OE19, DNMTi-HDACi Rep2 OE19, DNMTi-HDACi
- GSM8036454 OE19, DNMTi-HDACi Rep3 OE19, DNMTi-HDACi
- GSM8036455 GP5d p53-KO, DMSO Rep1 GP5d p53-KO, DMSO
- GSM8036456 GP5d p53-KO, DMSO Rep2 GP5d p53-KO, DMSO
- GSM8036457 GP5d p53-KO, DMSO Rep3 GP5d p53-KO, DMSO
- GSM8036458 GP5d p53-KO, DNMTi Rep1 GP5d p53-KO, DNMTi
- GSM8036459 GP5d p53-KO, DNMTi Rep2 GP5d p53-KO, DNMTi
- GSM8036460 GP5d p53-KO, DNMTi Rep3 GP5d p53-KO, DNMTi
- GSM8036461 GP5d p53-KO, HDACi Rep1 GP5d p53-KO, HDACi
- GSM8036462 GP5d p53-KO, HDACi Rep2 GP5d p53-KO, HDACi
- GSM8036463 GP5d p53-KO, HDACi Rep3 GP5d p53-KO, HDACi
- GSM8036464 GP5d p53-KO, SETDB1i Rep1 GP5d p53-KO, SETDB1i
- GSM8036465 GP5d p53-KO, SETDB1i Rep2 GP5d p53-KO, SETDB1i
- GSM8036466 GP5d p53-KO, SETDB1i Rep3 GP5d p53-KO, SETDB1i
- GSM8036467 GP5d p53-KO, DNMTi-HDACi Rep1 GP5d p53-KO, DNMTi-HDACi
- GSM8036468 GP5d p53-KO, DNMTi-HDACi Rep2 GP5d p53-KO, DNMTi-HDACi
- GSM8036469 GP5d p53-KO, DNMTi-HDACi Rep3 GP5d p53-KO, DNMTi-HDACi
- GSM8421509 LNCAP-1F5, DMSO Rep1 LNCAP-1F5, DMSO
+ 59 more — browse all 99 samples with per-sample file links →
- GSE254244 Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes 112 samples shares type-specific, derepression, transposable, inhibition, chromatin, elements, modifier, enzymes
- GSE283597 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq] 45 samples shares transposable, elements
- GSE261306 Early Prediction of Preeclampsia Based on Transposable Elements Deregulation in the Placenta [RNA-Seq] 30 samples shares transposable, elements
- GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares transposable, elements
- GSE283600 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development 83 samples shares transposable, elements
- GSE193413 Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [Hi-C] 28 samples shares inhibition, chromatin
- GSE244396 Binding Changes in Chromatin Factors Upon Targeted XPO1 Inhibition in T Cells 20 samples shares inhibition, chromatin
- GSE241598 Proteasome inhibition reprograms chromatin landscape in breast cancer (ChIP-Seq) 18 samples shares inhibition, chromatin
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.