Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 79 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
- 79 samples: 79 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
- Mutant FOXO1 controls an oncogenic network via enhancer accessibilityCell genomics · 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 GSE243499_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 PRJNA1018658 and SRA study SRP461555. 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 79 sample titles: 79 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.
- GSM7789518 ATACseq_NUDUL1_FOXO1_FKBP_0hA
- GSM7789519 ATACseq_NUDUL1_FOXO1_FKBP_0hB
- GSM7789520 ATACseq_NUDUL1_FOXO1_FKBP_0.25hA
- GSM7789521 ATACseq_NUDUL1_FOXO1_FKBP_0.25hB
- GSM7789522 ATACseq_NUDUL1_FOXO1_FKBP_0.5hA
- GSM7789523 ATACseq_NUDUL1_FOXO1_FKBP_0.5hB
- GSM7789524 ATACseq_NUDUL1_FOXO1_FKBP_1hA
- GSM7789525 ATACseq_NUDUL1_FOXO1_FKBP_1hB
- GSM7789526 ATACseq_NUDUL1_FOXO1_FKBP_2hA
- GSM7789527 ATACseq_NUDUL1_FOXO1_FKBP_2hB
- GSM7789528 ATACseq_OCILY1_FOXO1_FKBP_0hA
- GSM7789529 ATACseq_OCILY1_FOXO1_FKBP_0hB
- GSM7789530 ATACseq_OCILY1_FOXO1_FKBP_0.25hA
- GSM7789531 ATACseq_OCILY1_FOXO1_FKBP_0.25hB
- GSM7789532 ATACseq_OCILY1_FOXO1_FKBP_0.5hA
- GSM7789533 ATACseq_OCILY1_FOXO1_FKBP_0.5hB
- GSM7789534 ATACseq_OCILY1_FOXO1_FKBP_1hA
- GSM7789535 ATACseq_OCILY1_FOXO1_FKBP_1hB
- GSM7789536 ATACseq_OCILY1_FOXO1_FKBP_2hA
- GSM7789537 ATACseq_OCILY1_FOXO1_FKBP_2hB
- GSM7789538 ATACseq_SUDHL4_FOXO1_FKBP_0hA
- GSM7789539 ATACseq_SUDHL4_FOXO1_FKBP_0hB
- GSM7789540 ATACseq_SUDHL4_FOXO1_FKBP_0.5hA
- GSM7789541 ATACseq_SUDHL4_FOXO1_FKBP_0.5hB
- GSM7789542 ATACseq_SUDHL4_FOXO1_FKBP_1hA
- GSM7789543 ATACseq_SUDHL4_FOXO1_FKBP_1hB
- GSM7789544 ATACseq_SUDHL4_FOXO1_FKBP_2hA
- GSM7789545 ATACseq_SUDHL4_FOXO1_FKBP_2hB
- GSM7789546 ATACseq_SUDHL4_FOXO1_FKBP_2hC
- GSM7789547 RNAseq_NUDUL1_parA
- GSM7789548 RNAseq_NUDUL1_parB
- GSM7789549 RNAseq_NUDUL1_FOXO1_FKBP_0hA
- GSM7789550 RNAseq_NUDUL1_FOXO1_FKBP_0hB
- GSM7789551 RNAseq_NUDUL1_FOXO1_FKBP_6hA
- GSM7789552 RNAseq_NUDUL1_FOXO1_FKBP_6hB
- GSM7789553 RNAseq_NUDUL1_FOXO1_FKBP_24hA
- GSM7789554 RNAseq_NUDUL1_FOXO1_FKBP_24hB
- GSM7789555 RNAseq_OCILY1_parA
- GSM7789556 RNAseq_OCILY1_parB
- GSM7789557 RNAseq_OCILY1_FOXO1_FKBP_0hA
+ 39 more — browse all 79 samples with per-sample file links →
- GSE245686 Iron-Dependent KDM4D Activity Controls the Quiescence-Activity Balance of MSCs via the PI3K-Akt-Foxo1 Pathway 13 samples shares foxo1, controls
- GSE229542 Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma 199 samples shares oncogenic, controls
- GSE218269 CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release 100 samples shares polymerase, release
- GSE265883 Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (CUT&RUN) 68 samples shares polymerase, release
- GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 samples shares oncogenic, enhancer
- GSE214916 Enhancer engagement sustains oncogenic transformation and progression of B-cell precursor acute lymphoblastic leukemia 57 samples shares oncogenic, enhancer
- GSE280208 A CDK11-dependent RNA polymerase II pause-release checkpoint precedes CDK9-mediated transition to transcriptional elongation [ChIP-Seq] 33 samples shares polymerase, release
- GSE293856 Alphavirus M1 disrupts super-enhancer-driven oncogenic transcription in osteosarcoma [RNA-seq] 32 samples shares oncogenic, enhancer
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.