Epigenetic Activation and alteration of chromatin structure regulated by NSD2 in metastatic castration-resistant prostate cancer (ChIP-seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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
- 15 samples: 13 distinct titles, 2 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
- Chromatin activation with H3K36me2 and compartment shift in metastatic castration-resistant prostate cancerCancer letters · 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 GSE248629_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 PRJNA1045283 and SRA study SRP474252. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 15 sample titles: 13 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.
- GSM7918229 PC3_H3K4me1
- GSM7918230 PC3_H3K4me3
- GSM7918231 PC3_H3K27ac
- GSM7918232 LNCaP_H3K27me3
- GSM7918233 LNCaP_H3K36me2
- GSM7918234 PC3_H3K36me2
- GSM7918235 PC3_NSD2
- GSM7918236 LNCaP_NSD2
- GSM7918237 PC3_H3K27me3
- GSM7918238 DU145_H3K4me1
- GSM7918239 DU145_H3K4me3
- GSM7918240 DU145_H3K27ac
- GSM7918241 DU145_H3K36me2
- GSM7918242 DU145_H3K27me3
- GSM7918243 DU145_NSD2
- GSE309979 GeoMx GeoMx-DSP Toxic Lipid-induced Epigenetic Activation of ICAM1 in Liver Sinusoidal Endothelium Regulates Myeloid-Driven Fibro-inflammatory Response in MASH 217 samples shares epigenetic, activation
- GSE303855 Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen 45 samples shares epigenetic, chromatin
- GSE324815 Intratumoral CD40 agonist sotigalimab in combination with pembrolizumab induces rapid activation of antigen presenting cells and drives anti-tumor responses in non-injected tumors in metastatic melanoma: Results of a phase 1/2 study 24 samples shares activation, metastatic
- GSE282458 Regulation of epigenetics and chromosome structure by human ORC2 [ORC2 ChECseq] 18 samples shares epigenetic, structure
- GSE282576 Regulation of epigenetics and chromosome structure by human ORC2 [ORC5 ChECseq] 18 samples shares epigenetic, structure
- GSE282575 Regulation of epigenetics and chromosome structure by human ORC2 [ORC1 ChECseq] 18 samples shares epigenetic, structure
- GSE230342 Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC) 6 samples shares activation, chromatin
- GSE294275 Transcriptional analysis of direct NSD2 target genes in t(4;14) multiple myeloma reveals H3K36me2-dependent regulation and H3K27me3 antagonism [CUT&TAG] 40 samples shares nsd2
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.