Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 21 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
- Prostate cancerThis series is part of our curated briefing on it.
- Samples
- 21 samples: 21 samples, each with a distinct title — no replicated groupsGroups 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
- TP63-TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancerEpigenetics & chromatin · 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 GSE204813_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 PRJNA842380 and SRA study SRP377070. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 21 sample titles: 21 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.
- GSM6195513 PC3 OE GFP rep1 [methylation]
- GSM6195514 PC3 OE TP63 rep1 [methylation]
- GSM6195515 PC3 OE GFP rep2 [methylation]
- GSM6195516 PC3 OE TP63 rep2 [methylation]
- GSM6195517 RWPE-1 knockdown cntr rep 1 [RWPE1_LUC1]
- GSM6195518 RWPE-1 knockdown cntr rep 2 [RWPE1_LUC2]
- GSM6195519 RWPE-1 knockdown TRIM29 rep 1 [RWPE1_siTRIM29_1]
- GSM6195520 RWPE-1 knockdown TP63 rep 1 [RWPE1_siTP63_1]
- GSM6195521 RWPE-1 knockdown TP63 rep 2 [RWPE1_siTP63_2]
- GSM6195522 PC3 TP63 and TRIM29 overexpression rep2 [PC3_OE_TP63_TRIM29_2]
- GSM6195523 PC3 TP63 and TRIM29 overexpression rep1 [PC3_OE_TP63_TRIM29_1]
- GSM6195524 PC3 empty vector rep1 [PC3_OE_cntr_1]
- GSM6195525 PC3 empty vector rep2 [PC3_OE_cntr_2]
- GSM6195526 PC3 TP63 overexpression rep1 [PC3_OE_TP63_1]
- GSM6195527 PC3 TP63 overexpression rep2 [PC3_OE_TP63_2]
- GSM6195528 PC3 TRIM29 overexpression rep2 [PC3_OE_TRIM29_2]
- GSM6195529 PC3 TRIM29 overexpression rep1 [PC3_OE_TRIM29_1]
- GSM6195530 RWPE-1 IgG
- GSM6195531 RWPE-1 abTP63
- GSM6195532 PC3 OE TP63 IgG
- GSM6195533 PC3 OE TP63 ab TP63
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing
- GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing
- GSE304097 DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression 293 samples shares methylation, cluster
- GSE275738 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells 72 samples shares methylation, enhancers
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.