Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [cutandtag]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 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
- 14 samples: 4 × H3K4_sc vs 4 × H3K4_93v vs 3 × H3K9_sc vs 3 × H3K9_93vGroups 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
- Cancer cells subvert the primate-specific KRAB zinc finger protein ZNF93 to control APOBEC3BProceedings of the National Academy of Sciences of the United States of America · 2025
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 GSE290773_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 PRJNA1230089 and SRA study SRP567197. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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.
- GSM8821420 H3K9_scr2 H3K9_sc
- GSM8821421 H3K9_scr3 H3K9_sc
- GSM8821422 H3K9_scr4 H3K9_sc
- GSM8821423 H3K9_93v2 H3K9_93v
- GSM8821424 H3K9_93v3 H3K9_93v
- GSM8821425 H3K9_93v4 H3K9_93v
- GSM8821426 H3K4_scr1 H3K4_sc
- GSM8821427 H3K4_scr2 H3K4_sc
- GSM8821428 H3K4_scr3 H3K4_sc
- GSM8821429 H3K4_scr4 H3K4_sc
- GSM8821430 H3K4_93v1 H3K4_93v
- GSM8821431 H3K4_93v2 H3K4_93v
- GSM8821432 H3K4_93v3 H3K4_93v
- GSM8821433 H3K4_93v4 H3K4_93v
- GSE290771 Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [RNA-seq_2] 12 samples shares apobec3b, znf93, surveillance, epigenetic, sentinels, subvert, control
- GSE291537 Epigenetically controlled ZEB2 expression promotes the cytotoxic potential of CMV-specific CD8+ T cells 12 samples shares epigenetic, control
- GSE193234 R-loop editing by DNA cytosine deaminase APOBEC3B determines activities of estrogen receptor enhancers. 84 samples shares apobec3b
- GSE256495 Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia 195 samples shares epigenetic
- GSE271752 Macromolecular interactions dictate Polycomb-mediated epigenetic repression [ChIP-seq] 194 samples shares epigenetic
- GSE279619 SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation. 124 samples shares epigenetic
- GSE339365 Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19 120 samples shares epigenetic
- GSE287042 Epigenetic landscape of synthetic human centromeres: Euchromatic modifications coexist interdependently at CENP-A dense regions and prevent intrusion of other modifications [ChIP-seq] 102 samples shares epigenetic
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.