Chromatin accessibility and transcriptomic responses to HDAC inhibitors in TP53 mutated patient-derived colon cancer organoids [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- 12 samples: 6 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
- Changes in chromatin accessibility and transcriptional landscape induced by HDAC inhibitors in TP53 mutated patient-derived colon cancer organoidsBiomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 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 GSE246044_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 PRJNA1031174 and SRA study SRP467988. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7854451 PDO19 (control) ATAC-seq rep 1 PDO19 (control) ATAC-seq
- GSM7854452 PDO19 SAHA ATAC-seq rep1 PDO19 SAHA ATAC-seq
- GSM7854453 PDO19 NKL54 ATAC-seq rep1 PDO19 NKL54 ATAC-seq
- GSM7854454 PDO71 (control) ATAC-seq rep 1 PDO71 (control) ATAC-seq
- GSM7854455 PDO71 SAHA ATAC-seq rep1 PDO71 SAHA ATAC-seq
- GSM7854456 PDO71 NKL54 ATAC-seq rep1 PDO71 NKL54 ATAC-seq
- GSM7854457 PDO19 (control) ATAC-seq rep 2 PDO19 (control) ATAC-seq
- GSM7854458 PDO19 SAHA ATAC-seq rep 2 PDO19 SAHA ATAC-seq
- GSM7854459 PDO19 NKL54 ATAC-seq rep2 PDO19 NKL54 ATAC-seq
- GSM7854460 PDO71 (control) ATAC-seq rep 2 PDO71 (control) ATAC-seq
- GSM7854461 PDO71 SAHA ATAC-seq rep2 PDO71 SAHA ATAC-seq
- GSM7854462 PDO71 NKL54 ATAC-seq rep2 PDO71 NKL54 ATAC-seq
- GSE301514 ID3 Deficiency Alters Chromatin Accessibility at DSB Sites and Enhances Vulnerability to HDAC Inhibition [ATAC-seq] 12 samples shares hdac, accessibility, chromatin, atac-seq
- GSE291386 Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq] 165 samples shares accessibility, chromatin, atac-seq
- GSE318082 BAF complexes maintain accessibility at stimulus-responsive chromatin and are required for transcriptional stimulus responses [ATAC-seq] 63 samples shares accessibility, chromatin, atac-seq
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares accessibility, chromatin, atac-seq
- GSE240183 HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype [ATAC-seq] 22 samples shares accessibility, chromatin, atac-seq
- GSE290342 Caloric restriction mimetic 2-deoxyglucose alters metabolic and transcriptomic phenotype in association with changes in chromatin accessibility in human astrocytes [ATAC-Seq] 12 samples shares accessibility, chromatin, atac-seq
- GSE277922 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids 25 samples shares accessibility, chromatin, organoids
- GSE305560 TP53-Agnostic Lethality through Combined Pan-HDAC and CDK Inhibition in Acute Myeloid Leukemia 18 samples shares hdac, tp53
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.