Chromatin accessibility and transcriptomic responses to HDAC inhibitors in TP53 mutated patient-derived colon cancer organoids
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 30 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)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 30 samples: 24 distinct titles, 6 of them repeatedGroups 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
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 GSE246046_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 PRJNA1031172 and SRA study SRP467988. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 30 sample titles: 24 distinct titles with little repetition. 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
- GSM7854452 PDO19 SAHA ATAC-seq rep1
- GSM7854453 PDO19 NKL54 ATAC-seq rep1
- GSM7854454 PDO71 (control) ATAC-seq rep 1
- GSM7854455 PDO71 SAHA ATAC-seq rep1
- GSM7854456 PDO71 NKL54 ATAC-seq rep1
- GSM7854457 PDO19 (control) ATAC-seq rep 2
- GSM7854458 PDO19 SAHA ATAC-seq rep 2
- GSM7854459 PDO19 NKL54 ATAC-seq rep2
- GSM7854460 PDO71 (control) ATAC-seq rep 2
- GSM7854461 PDO71 SAHA ATAC-seq rep2
- GSM7854462 PDO71 NKL54 ATAC-seq rep2
- GSM7854463 PDO19 (control) rep 1 [1740R-251-01]
- GSM7854464 PDO19 SAHA rep1 [1740R-251-02]
- GSM7854465 PDO19 NKL54 rep1 [1740R-251-03]
- GSM7854466 PDO71 (control) rep 1 [1740R-251-04]
- GSM7854467 PDO71 SAHA rep1 [1740R-251-05]
- GSM7854468 PDO71 NKL54 rep1 [1740R-251-06]
- GSM7854469 PDO19 (control) rep 2 [1740R-251-07]
- GSM7854470 PDO19 SAHA rep2 [1740R-251-08]
- GSM7854471 PDO19 NKL54 rep2 [1740R-251-09]
- GSM7854472 PDO71 (control) rep 2 [1740R-251-10]
- GSM7854473 PDO71 SAHA rep2 [1740R-251-11]
- GSM7854474 PDO71 NKL54 rep2 [1740R-251-12]
- GSM7854475 PDO19 (control) rep 3 [1740R-251-13]
- GSM7854476 PDO19 SAHA rep3 [1740R-251-14]
- GSM7854477 PDO19 NKL54 rep3 [1740R-251-15]
- GSM7854478 PDO71 (control) rep 3 [1740R-251-16]
- GSM7854479 PDO71 SAHA rep3 [1740R-251-17]
- GSM7854480 PDO71 NKL54 rep3 [1740R-251-18]
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing
- GSE301514 ID3 Deficiency Alters Chromatin Accessibility at DSB Sites and Enhances Vulnerability to HDAC Inhibition [ATAC-seq] 12 samples shares hdac, accessibility, chromatin
- 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
- GSE251754 Simultaneous profiling of full-length RNA transcripts and chromatin accessibility within single cells of human retinal organoids 10 samples shares accessibility, chromatin, organoids
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.