Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors (ATAC-Seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 45 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
- 45 samples: 10 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
- Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivorsNature communications · 2024
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 GSE254753_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 PRJNA1071623 and SRA study SRP487188. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 25 samples.
How we read this: 10 replicated groups read from 45 sample titles; they account for 25 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.
- GSM8057187 Bulk ATAC-seq RS2_RT-
- GSM8057188 Bulk ATAC-seq RS2_RT+
- GSM8057189 Bulk ATAC-seq RS3_RT-
- GSM8057190 Bulk ATAC-seq RS3_RT+
- GSM8057191 Bulk ATAC-seq RS4_RT-
- GSM8057192 Bulk ATAC-seq RS4_RT+
- GSM8057193 Bulk ATAC-seq RS5_RT-
- GSM8057194 Bulk ATAC-seq RS5_RT+
- GSM8057195 Bulk ATAC-seq RS6_RT-
- GSM8057196 Bulk ATAC-seq RS6_RT+
- GSM8057197 Bulk ATAC-seq RS17_RT-
- GSM8057198 Bulk ATAC-seq RS17_RT+
- GSM8057199 Bulk ATAC-seq RS26_RT-
- GSM8057200 Bulk ATAC-seq RS26_RT+
- GSM8057201 Bulk ATAC-seq Ctr_D1_1 Bulk ATAC-seq Ctr_D1
- GSM8057202 Bulk ATAC-seq Ctr_D1_2 Bulk ATAC-seq Ctr_D1
- GSM8057203 Bulk ATAC-seq IR_D1_1 Bulk ATAC-seq IR_D1
- GSM8057204 Bulk ATAC-seq IR_D1_2 Bulk ATAC-seq IR_D1
- GSM8057205 Bulk ATAC-seq Ctr_D7_1 Bulk ATAC-seq Ctr_D7
- GSM8057206 Bulk ATAC-seq Ctr_D7_2 Bulk ATAC-seq Ctr_D7
- GSM8057207 Bulk ATAC-seq IR_D7_1 Bulk ATAC-seq IR_D7
- GSM8057208 Bulk ATAC-seq IR_D7_2 Bulk ATAC-seq IR_D7
- GSM8349818 Bulk ATAC-seq RS47 RT- S-
- GSM8349819 Bulk ATAC-seq RS47 RT- S+
- GSM8349820 Bulk ATAC-seq RS48 RT- S-
- GSM8349821 Bulk ATAC-seq RS48 RT- S+
- GSM8349822 Bulk ATAC-seq RS49 RT- S-
- GSM8349823 Bulk ATAC-seq RS49 RT- S+
- GSM8349824 Bulk ATAC-seq Ctr_D14_1 Bulk ATAC-seq Ctr_D14
- GSM8349825 Bulk ATAC-seq Ctr_D14_2 Bulk ATAC-seq Ctr_D14
- GSM8349826 Bulk ATAC-seq Ctr_D14_3 Bulk ATAC-seq Ctr_D14
- GSM8349827 Bulk ATAC-seq IR_D14_1 Bulk ATAC-seq IR_D14
- GSM8349828 Bulk ATAC-seq IR_D14_2 Bulk ATAC-seq IR_D14
- GSM8349829 Bulk ATAC-seq IR_D14_3 Bulk ATAC-seq IR_D14
- GSM8349830 Bulk ATAC-seq Ctr dermal fibroblasts 1 Bulk ATAC-seq Ctr derma…
- GSM8349831 Bulk ATAC-seq Ctr dermal fibroblasts 2 Bulk ATAC-seq Ctr derma…
- GSM8349832 Bulk ATAC-seq IR dermal fibroblasts D1-1 Bulk ATAC-seq IR dermal…
- GSM8349833 Bulk ATAC-seq IR dermal fibroblasts D1-2 Bulk ATAC-seq IR dermal…
- GSM8349834 Bulk ATAC-seq IR dermal fibroblasts D1-3 Bulk ATAC-seq IR dermal…
- GSM8349835 Bulk ATAC-seq Ctr dermal cell 1 Bulk ATAC-seq Ctr derma…
+ 5 more — browse all 45 samples with per-sample file links →
- GSE281868 Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (ATAC-Seq_2) 12 samples shares fibroblasts, epigenetic, atac-seq
- GSE291280 Cardiac Radiotherapy-Induced Epigenetic Memory Underlies Electrophysiologic and Metabolic Reprogramming [RNA-seq] 108 samples shares radiotherapy, epigenetic, memory
- GSE264696 Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [CITE-seq] 16 samples shares epigenetic, memory
- GSE287736 Sex-specific KDM6A-HNF4A-CREBH network controls lipoprotein cholesterol metabolism and atherosclerosis via epigenetic reprograming of hepatocytes 138 samples shares epigenetic
- GSE282436 Development of a potent epigenetic editor targeting human PCSK9 with durable reduction of cholesterol in mice and non-human primates [hybrid capture methylseq] 66 samples shares epigenetic
- GSE299380 KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [CUT&Run] 33 samples shares epigenetic
- GSE255802 Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (Cut&Tag) 20 samples shares epigenetic
- GSE239815 Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs 307 samples shares epigenetic
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.