Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [SuperSeries]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 160 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
- 160 samples: 80 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
- Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organizationNucleic acids research · 2025
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 GSE279021_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 PRJNA1169930. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 160 samples.
How we read this: 80 replicated groups read from 160 sample titles; they account for 160 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.
- GSM8559095 A549_CTRL_input_Rep1 A549_CTRL_input
- GSM8559096 A549_CTRL_input_Rep2 A549_CTRL_input
- GSM8559097 A549_CTRL_p53_Rep1 A549_CTRL_p53
- GSM8559098 A549_CTRL_p53_Rep2 A549_CTRL_p53
- GSM8559099 A549_NUT_input_Rep1 A549_NUT_input
- GSM8559100 A549_NUT_input_Rep2 A549_NUT_input
- GSM8559101 A549_NUT_p53_Rep1 A549_NUT_p53
- GSM8559102 A549_NUT_p53_Rep2 A549_NUT_p53
- GSM8559103 GM12878_CTRL_input_Rep1 GM12878_CTRL_input
- GSM8559104 GM12878_CTRL_input_Rep2 GM12878_CTRL_input
- GSM8559105 GM12878_CTRL_p53_Rep1 GM12878_CTRL_p53
- GSM8559106 GM12878_CTRL_p53_Rep2 GM12878_CTRL_p53
- GSM8559107 GM12878_NUT_input_Rep1 GM12878_NUT_input
- GSM8559108 GM12878_NUT_input_Rep2 GM12878_NUT_input
- GSM8559109 GM12878_NUT_p53_Rep1 GM12878_NUT_p53
- GSM8559110 GM12878_NUT_p53_Rep2 GM12878_NUT_p53
- GSM8559111 HCT116_CTRL_input_Rep1 HCT116_CTRL_input
- GSM8559112 HCT116_CTRL_input_Rep2 HCT116_CTRL_input
- GSM8559113 HCT116_CTRL_p53_Rep1 HCT116_CTRL_p53
- GSM8559114 HCT116_CTRL_p53_Rep2 HCT116_CTRL_p53
- GSM8559115 HCT116_NUT_input_Rep1 HCT116_NUT_input
- GSM8559116 HCT116_NUT_input_Rep2 HCT116_NUT_input
- GSM8559117 HCT116_NUT_p53_Rep1 HCT116_NUT_p53
- GSM8559118 HCT116_NUT_p53_Rep2 HCT116_NUT_p53
- GSM8559119 HEK293_CTRL_input_Rep1 HEK293_CTRL_input
- GSM8559120 HEK293_CTRL_input_Rep2 HEK293_CTRL_input
- GSM8559121 HEK293_CTRL_p53_Rep1 HEK293_CTRL_p53
- GSM8559122 HEK293_CTRL_p53_Rep2 HEK293_CTRL_p53
- GSM8559123 HEK293_NUT_input_Rep1 HEK293_NUT_input
- GSM8559124 HEK293_NUT_input_Rep2 HEK293_NUT_input
- GSM8559125 HEK293_NUT_p53_Rep1 HEK293_NUT_p53
- GSM8559126 HEK293_NUT_p53_Rep2 HEK293_NUT_p53
- GSM8559127 HeLa_CTRL_input_Rep1 HeLa_CTRL_input
- GSM8559128 HeLa_CTRL_input_Rep2 HeLa_CTRL_input
- GSM8559129 HeLa_CTRL_p53_Rep1 HeLa_CTRL_p53
- GSM8559130 HeLa_CTRL_p53_Rep2 HeLa_CTRL_p53
- GSM8559131 HeLa_NUT_input_Rep1 HeLa_NUT_input
- GSM8559132 HeLa_NUT_input_Rep2 HeLa_NUT_input
- GSM8559133 HeLa_NUT_p53_Rep1 HeLa_NUT_p53
- GSM8559134 HeLa_NUT_p53_Rep2 HeLa_NUT_p53
+ 120 more — browse all 160 samples with per-sample file links →
- GSE278977 Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [ChIP-seq] 80 samples shares organization, p53-induced, distinctive, programs, identity, features, spatial
- GSE278979 Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [RNA-seq] 40 samples shares organization, p53-induced, distinctive, programs, identity, features, spatial
- GSE281260 Spatially organized inflammatory myeloid-CD8+ T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment 146 samples shares organization, spatial
- GSE300798 Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord [snRNA-seq] 68 samples shares organization, spatial
- GSE300791 Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord [scRNA-seq] 20 samples shares organization, spatial
- GSE300786 Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord [snATAC-seq] 20 samples shares organization, spatial
- GSE300782 Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord [ATAC-seq] 20 samples shares organization, spatial
- GSE300809 Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord [STABseq] 16 samples shares organization, spatial
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.