Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context [ChIP-seq; 4C-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 14 distinct titles, 4 of them repeatedGroups 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 GSE299353_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 PRJNA1273963 and SRA study SRP590837. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 sample titles: 14 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.
- GSM9037945 K562 cells, LP recombination, WT_eNMU, rep1 (ChIP)
- GSM9037946 K562 cells, LP recombination, WT_eNMU, rep2 (ChIP)
- GSM9037947 K562 cells, LP recombination, e1_mGATA1, rep1 (ChIP)
- GSM9037948 K562 cells, LP recombination, e1_mGATA1, rep2 (ChIP)
- GSM9037949 K562 cells, LP recombination, e1_mRUNX1, rep1 (ChIP)
- GSM9037950 K562 cells, LP recombination, e1_mRUNX1, rep2 (ChIP)
- GSM9037951 K562 cells, LP recombination, e2_mSTAT5, rep1 (ChIP)
- GSM9037952 K562 cells, LP recombination, e2_mSTAT5, rep2 (ChIP)
- GSM9037953 K562 cells, LP recombination, e1_mGATA1, rep1 (Input)
- GSM9037954 K562 cells, LP recombination, WT_eNMU, rep2 (Input)
- GSM9727198 K562 cells, wildtype, rep1
- GSM9727199 K562 cells, wildtype, rep2
- GSM9727200 K562 cells, eNMU deletion, rep1
- GSM9727201 K562 cells, eNMU deletion, rep2
- GSM9727202 K562 cells, e2 deletion, Clone 1, rep1
- GSM9727203 K562 cells, e2 deletion, Clone 1, rep2
- GSM9727204 K562 cells, e2 deletion, Clone 15, rep1
- GSM9727205 K562 cells, e2 deletion, Clone 15, rep2
- GSE294036 Human Papillomavirus Genomes Associate with Active Host Chromatin during Viral Genome Maintenance [4C-seq] 7 samples shares 4c-seq, chromatin
- GSE290054 H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq] 35 samples shares regulatory, chip-seq
- GSE277922 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids 25 samples shares regulatory, chromatin
- GSE260528 Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [ChIP-seq] 20 samples shares regulatory, chip-seq
- GSE314625 WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [mRNA-seq] 18 samples shares regulatory, chromatin
- GSE286472 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [human_Treg_ChIP-seq] 18 samples shares regulatory, chip-seq
- GSE300986 Interplay between CoREST, p300 and retinoic acid signaling in Acute myeloid leukemia [ChIP-seq] 12 samples shares interplay, chip-seq
- GSE247982 The chromatin landscape of high-grade serous ovarian cancer metastasis identifies potential regulatory drivers of chemoresistant tumour cells 10 samples shares regulatory, chromatin
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.