Charting the regulatory landscape of TP53 on transposable elements in cancer [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples: 12 conditions, mostly in duplicateGroups 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
- Charting the regulatory landscape of TP53 on transposable elements in cancerGenome research · 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 GSE262051_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1090105 and SRA study SRP496774. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 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.
- GSM8156624 A549_KO_DMSO_ATAC-seq_BRep1 A549_KO_DMSO_ATAC-seq_B
- GSM8156625 A549_KO_DMSO_ATAC-seq_BRep2 A549_KO_DMSO_ATAC-seq_B
- GSM8156626 A549_KO_DOX_ATAC-seq_BRep1 A549_KO_DOX_ATAC-seq_B
- GSM8156627 A549_KO_DOX_ATAC-seq_BRep2 A549_KO_DOX_ATAC-seq_B
- GSM8156628 A549_WT_DMSO_ATAC-seq_BRep1 A549_WT_DMSO_ATAC-seq_B
- GSM8156629 A549_WT_DMSO_ATAC-seq_BRep2 A549_WT_DMSO_ATAC-seq_B
- GSM8156630 A549_WT_DOX_ATAC-seq_BRep1 A549_WT_DOX_ATAC-seq_B
- GSM8156631 A549_WT_DOX_ATAC-seq_BRep2 A549_WT_DOX_ATAC-seq_B
- GSM8156632 HCT116_KO_DMSO_ATAC-seq_BRep1 HCT116_KO_DMSO_ATAC-seq…
- GSM8156633 HCT116_KO_DMSO_ATAC-seq_BRep2 HCT116_KO_DMSO_ATAC-seq…
- GSM8156634 HCT116_KO_DOX_ATAC-seq_BRep1 HCT116_KO_DOX_ATAC-seq_B
- GSM8156635 HCT116_KO_DOX_ATAC-seq_BRep2 HCT116_KO_DOX_ATAC-seq_B
- GSM8156636 HCT116_WT_DMSO_ATAC-seq_BRep1 HCT116_WT_DMSO_ATAC-seq…
- GSM8156637 HCT116_WT_DMSO_ATAC-seq_BRep2 HCT116_WT_DMSO_ATAC-seq…
- GSM8156638 HCT116_WT_DOX_ATAC-seq_BRep1 HCT116_WT_DOX_ATAC-seq_B
- GSM8156639 HCT116_WT_DOX_ATAC-seq_BRep2 HCT116_WT_DOX_ATAC-seq_B
- GSM8156640 RKO_KO_DMSO_ATAC-seq_BRep1 RKO_KO_DMSO_ATAC-seq_B
- GSM8156641 RKO_KO_DMSO_ATAC-seq_BRep2 RKO_KO_DMSO_ATAC-seq_B
- GSM8156642 RKO_KO_DOX_ATAC-seq_BRep1 RKO_KO_DOX_ATAC-seq_B
- GSM8156643 RKO_KO_DOX_ATAC-seq_BRep2 RKO_KO_DOX_ATAC-seq_B
- GSM8156644 RKO_WT_DMSO_ATAC-seq_BRep1 RKO_WT_DMSO_ATAC-seq_B
- GSM8156645 RKO_WT_DMSO_ATAC-seq_BRep2 RKO_WT_DMSO_ATAC-seq_B
- GSM8156646 RKO_WT_DOX_ATAC-seq_BRep1 RKO_WT_DOX_ATAC-seq_B
- GSM8156647 RKO_WT_DOX_ATAC-seq_BRep2 RKO_WT_DOX_ATAC-seq_B
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares regulatory, elements
- GSE254244 Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes 112 samples shares transposable, elements
- GSE290054 H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq] 35 samples shares regulatory, elements
- GSE278245 Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers 21 samples shares regulatory, elements
- GSE275737 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [ChIP-Seq] 21 samples shares transposable, elements
- GSE325670 Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects 140 samples shares regulatory, elements
- GSE283600 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development 83 samples shares transposable, elements
- GSE283597 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq] 45 samples shares transposable, elements
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.