Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 6 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
- Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistanceNature communications · 2024
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 GSE268228_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 PRJNA1115203 and SRA study SRP509460. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 16 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.
- GSM8288246 REC-1, DMSO, ATAC, Repeat 1 REC-1, DMSO, ATAC, Repe…
- GSM8288247 REC-1, DMSO, ATAC, Repeat 2 REC-1, DMSO, ATAC, Repe…
- GSM8288248 REC-1, DMSO, ATAC, Repeat 3 REC-1, DMSO, ATAC, Repe…
- GSM8288249 REC-1, Ibrutinib Resistant, ATAC, Repeat 1 REC-1, Ibrutinib Resist…
- GSM8288250 REC-1, Ibrutinib Resistant, ATAC, Repeat 2 REC-1, Ibrutinib Resist…
- GSM8288251 REC-1, Ibrutinib Resistant, ATAC, Repeat 3 REC-1, Ibrutinib Resist…
- GSM8288252 REC-1, DMSO, H3K27ac ChIP-seq, Repeat 1 REC-1, DMSO, H3K27ac Ch…
- GSM8288253 REC-1, DMSO, H3K27ac ChIP-seq, Repeat 2 REC-1, DMSO, H3K27ac Ch…
- GSM8288254 REC-1, Ibrutinib Resistant, H3K27ac ChIP, Repeat 1 REC-1, Ibrutinib Resist…
- GSM8288255 REC-1, Ibrutinib Resistant, H3K27ac ChIP, Repeat 2 REC-1, Ibrutinib Resist…
- GSM8288256 REC-1, DMSO, Hi-C
- GSM8288257 REC-1, Ibrutinib Resistant, Hi-C
- GSM8288258 REC-1, DMSO, RNA-seq, Repeat 1 REC-1, DMSO, RNA-seq, R…
- GSM8288259 REC-1, DMSO, RNA-seq, Repeat 2 REC-1, DMSO, RNA-seq, R…
- GSM8288260 REC-1, DMSO, RNA-seq, Repeat 3 REC-1, DMSO, RNA-seq, R…
- GSM8288261 REC-1, Ibrutinib Resistant, RNA-seq, Repeat 1 REC-1, Ibrutinib Resist…
- GSM8288262 REC-1, Ibrutinib Resistant, RNA-seq, Repeat 2 REC-1, Ibrutinib Resist…
- GSM8288263 REC-1, Ibrutinib Resistant, RNA-seq, Repeat 3 REC-1, Ibrutinib Resist…
- GSE291147 Mapping convergent regulators of melanoma drug resistance by PerturbFate 320 samples shares resistance, drug
- GSE282258 Imaging-based drug screening combined with moleuclar profiling identifies signatures and drivers of therapy resistance in pediatric AML [ATAC-seq] 44 samples shares resistance, drug
- GSE282423 Imaging-based drug screening combined with moleuclar profiling identifies signatures and drivers of therapy resistance in pediatric AML [RNA-seq] 28 samples shares resistance, drug
- GSE212437 EZH2 reads DNA 6mA to regulate survival and drug resistance of human head and neck squamous carcinoma by suppressing RIOX2-CDKN1A-NRF2 signaling axis [MeDIP-ChIP-seq-shRNA] 17 samples shares resistance, drug
- GSE308647 Drug tolerant persisters and immunotherapy persister cells exhibit cross-resistance and share common survival mechanisms 15 samples shares resistance, drug
- GSE280381 Investigating therapy-induced senescence as a reversible escape mechanism of drug resistance in breast cancer cells using high-dose doxorubicin treatment 12 samples shares resistance, drug
- GSE279641 G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [CUT&Tag] 12 samples shares resistance, drug
- GSE199913 KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage 231 samples shares promoting
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.