Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [RNA-seq_2]
RNA-seq (gene expression) · human · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 3 × RF040_GFP_NoD vs 3 × RF040_GFP_D vs 3 × RF040_ZNF93_NoD vs 3 × RF040_ZNF93_DGroups 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 GSE290771_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1230072 and SRA study SRP567175. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 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.
- GSM8821384 RF040_GFP_NoD_Rep1 RF040_GFP_NoD
- GSM8821385 RF040_GFP_D_Rep1 RF040_GFP_D
- GSM8821386 RF040_GFP_NoD_Rep2 RF040_GFP_NoD
- GSM8821387 RF040_GFP_D_Rep2 RF040_GFP_D
- GSM8821388 RF040_GFP_NoD_Rep3 RF040_GFP_NoD
- GSM8821389 RF040_GFP_D_Rep3 RF040_GFP_D
- GSM8821390 RF040_ZNF93_NoD_Rep1 RF040_ZNF93_NoD
- GSM8821391 RF040_ZNF93_NoD_Rep2 RF040_ZNF93_NoD
- GSM8821392 RF040_ZNF93_NoD_Rep3 RF040_ZNF93_NoD
- GSM8821393 RF040_ZNF93_D_Rep1 RF040_ZNF93_D
- GSM8821394 RF040_ZNF93_D_Rep2 RF040_ZNF93_D
- GSM8821395 RF040_ZNF93_D_Rep3 RF040_ZNF93_D
- GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares epigenetic, rna-seq
- GSE289466 Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [RNA-seq] 98 samples shares epigenetic, rna-seq
- GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares epigenetic, rna-seq
- GSE306915 Integrated epigenetic and genetic programming of primary human T cells [RNA-seq] 77 samples shares epigenetic, rna-seq
- GSE282444 Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq] 56 samples shares epigenetic, rna-seq
- GSE248728 BCG vaccination impacts the epigenetic landscape of progenitor cells in human bone marrow (scRNA-Seq) 28 samples shares epigenetic, rna-seq
- GSE270505 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [RNA-seq] 19 samples shares epigenetic, rna-seq
- GSE291537 Epigenetically controlled ZEB2 expression promotes the cytotoxic potential of CMV-specific CD8+ T cells 12 samples shares epigenetic, control
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.