Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 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
- 17 samples: 8 conditions, mostly in duplicateGroups 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.
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 GSE203644_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 PRJNA841668 and SRA study SRP376722. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 17 sample titles; they account for 16 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.
- GSM7996338 U2OS_Input
- GSM7996341 U2OS_FOXA2FL_day4_biol rep1 U2OS_FOXA2FL_day4_biol
- GSM7996342 U2OS_FOXA2FL_day4_biol rep2 U2OS_FOXA2FL_day4_biol
- GSM7996345 U2OS_FOXA2dCTD_day4_biol rep1 U2OS_FOXA2dCTD_day4_biol
- GSM7996346 U2OS_FOXA2dCTD_day4_biol rep2 U2OS_FOXA2dCTD_day4_biol
- GSM7996347 U2OS_FOXA1FL_day4_bio rep1 U2OS_FOXA1FL_day4
- GSM7996348 U2OS_FOXA1FL_day4_bio rep2 U2OS_FOXA1FL_day4
- GSM7996349 U2OS_FOXA3FL_day4_biol rep1 U2OS_FOXA3FL_day4_biol
- GSM7996350 U2OS_FOXA3FL_day4_biol rep2 U2OS_FOXA3FL_day4_biol
- GSM7996351 U2OS_FOXA1dCTD_day4_biol rep1 U2OS_FOXA1dCTD_day4_biol
- GSM7996352 U2OS_FOXA1dCTD_day4_biol rep2 U2OS_FOXA1dCTD_day4_biol
- GSM7996353 U2OS_FOXA3dCTD_day4_biol rep1 U2OS_FOXA3dCTD_day4_biol
- GSM7996354 U2OS_FOXA3dCTD_day4_biol rep2 U2OS_FOXA3dCTD_day4_biol
- GSM7996355 U2OS_SOX2FL_day4_bio rep1 U2OS_SOX2FL_day4
- GSM7996356 U2OS_SOX2FL_day4_bio rep2 U2OS_SOX2FL_day4
- GSM7996357 U2OS_SOX2FLFOXA2CTD_day4_bio rep1 U2OS_SOX2FLFOXA2CTD_day4
- GSM7996358 U2OS_SOX2FLFOXA2CTD_day4_bio rep2 U2OS_SOX2FLFOXA2CTD_day4
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares transcription, chromatin, chip-seq
- GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 samples shares transcription, chip-seq, factors
- GSE284519 TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination [ChIP-seq] 93 samples shares transcription, chip-seq
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription, factors
- GSE335058 Evolutionary guided transcription factor design programs novel T cell states [ChIP-Seq] 66 samples shares transcription, chip-seq
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares transcription, chip-seq
- GSE259248 ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer (ChIP-Seq) 36 samples shares transcription, chip-seq
- GSE267597 AP-1 Mediates Oncogenic Transcription and Predicts Fatality in Lung Squamous Cell Carcinoma Patients [ChIP-seq] 36 samples shares transcription, chip-seq
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.