O-GlcNAcylation of FOXK1 co-opts BAP1 to orchestrate the E2F pathway and promote oncogenesis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 69 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
- 69 samples: 69 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
- O-GlcNAcylation of FOXK1 co-opts BAP1 to orchestrate the E2F pathway and promotes oncogenesisNature communications · 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 GSE260904_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 PRJNA1106527 and SRA study SRP505048. 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 69 sample titles: 69 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.
- GSM8244587 IMR90, input, ChIP
- GSM8244588 IMR90, endogenous FOXK1, ChIP
- GSM8244589 IMR90, endogenous FOXK2, ChIP
- GSM8244590 IMR90, vector, ChIP
- GSM8244591 IMR90, 3Flag FOXK1, ChIP
- GSM8244592 IMR90, 3Flag FOXK2, ChIP
- GSM8244593 IMR90, 3Flag FOXK1-7A, ChIP
- GSM8244594 IMR90, 3Flag FOXK1-11A, ChIP
- GSM8244595 U2OS, vector, ChIP
- GSM8244596 U2OS, input, ChIP
- GSM8244597 U2OS, 3Flag FOXK1, ChIP
- GSM8244598 U2OS, 3Flag FOXK1-7A, ChIP
- GSM8244599 U2OS, endogenous FOXK1, ChIP
- GSM8244600 K562, vector, ChIP
- GSM8244601 K562, Input, ChIP
- GSM8244602 K562, 3Flag FOXK1, ChIP
- GSM8244603 K562, 3Flag FOXK1-7A, ChIP
- GSM8244604 K562, 3Flag FOXK2, ChIP
- GSM8244605 IMR90, IgG_300523, Cut&Run, merge
- GSM8244606 IMR90, vector, siRNA anti-FOXK1, BAP1, Cut&Run, merge
- GSM8244607 IMR90, FOXK1, siRNA anti-FOXK1, BAP1, Cut&Run, merge
- GSM8244608 IMR90, FOXK1-7A, siRNA anti-FOXK1, BAP1, Cut&Run, merge
- GSM8244609 IMR90, FOXK1-11A, siRNA anti-FOXK1, BAP1, Cut&Run, merge
- GSM8244610 IMR90, IgG_170723, Cut&Run
- GSM8244611 IMR90, vector, siRNA anti-FOXK1, H2AUb, Cut&Run, merge
- GSM8244612 IMR90, FOXK1, siRNA anti-FOXK1, H2AUb, Cut&Run, merge
- GSM8244613 IMR90, FOXK1-7A, siRNA anti-FOXK1, H2AUb, Cut&Run, merge
- GSM8244614 IMR90, FOXK1-11A, siRNA anti-FOXK1, H2AUb, Cut&Run, merge
- GSM8244615 IMR90, vector, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge
- GSM8244616 IMR90, FOXK1, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge
- GSM8244617 IMR90, FOXK1-7A, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge
- GSM8244618 IMR90, FOXK1-11A, siRNA anti-FOXK1, H3K4me1, Cut&Run, merge
- GSM8773813 IMR90, FOXK1_G0, Cut&Run, merge
- GSM8773814 IMR90, FOXK1_T18, Cut&Run, merge
- GSM8773815 IMR90, FOXK2_G0, Cut&Run, merge
- GSM8773816 IMR90, FOXK2_T18, Cut&Run, merge
- GSM8773817 IMR90, IgG_synchro, Cut&Run
- GSM8773818 IMR90, IgG_forSIN3A, Cut&Run
- GSM8773819 IMR90, SIN3A_vector_siFOXK1, Cut&Run, merge
- GSM8773820 IMR90, SIN3A_FOXK1_siFOXK1, Cut&Run, merge
+ 29 more — browse all 69 samples with per-sample file links →
- GSE308040 AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma 42 samples shares e2f, orchestrate
- GSE273826 Non-catalytic role of SETD1A promotes gastric cancer cell proliferation through the E2F4-TAF6 axis in the cell cycle 30 samples shares e2f, promote
- GSE242227 H2A.Z chaperones promote melanoma cell growth by facilitating transcription of E2F target genes through H2A.Z deposition and H4 acetylation 30 samples shares e2f, promote
- GSE273824 Non-catalytic role of SETD1A promotes gastric cancer cell proliferation through the E2F4-TAF6 axis in the cell cycle (ChIP-seq) 24 samples shares e2f, promote
- GSE296929 E2F4/SETD1A axis-mediated METTL3 methylation promotes tumor immune evasion through impeding endogenous retroelements expression 18 samples shares e2f, promote
- GSE272538 A novel association of EZH2 and E2F1 promotes breast cancer cell proliferation through chromatin remodeling [RNA-Seq] 18 samples shares e2f, promote
- GSE308037 AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [ABC_AID_KO_RNA-seq] 18 samples shares e2f, orchestrate
- GSE291247 DLEU2 promotes cell motility and immune infiltration in cervical squamous cell carcinoma through reciprocal feed-forward activation of E2F1 16 samples shares e2f, promote
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.