RNA Polymerase II pausing enhances estrogen receptor-alpha binding on promoters in RNA-dependent manner
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 22 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
- 22 samples: 22 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
- Paused RNA polymerase primes promoters via RNA-mediated stabilisation of transcription factor ERαNature 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 GSE278896_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 PRJNA1169375 and SRA study SRP536820. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 11 as controls.
How we read this: Read from 22 sample titles: 22 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.
- GSM8556953 MCF7, DMSO Control for DRB, Rep1, ERalpha, ChIP
- GSM8556954 MCF7, DMSO Control for DRB, Rep2, ERalpha, ChIP
- GSM8556955 MCF7, DMSO Control for DRB, Rep1, Flag, RRGG_mt, ChIP
- GSM8556956 MCF7, DMSO Control for DRB, Rep2, Flag, RRGG_mt, ChIP
- GSM8556957 MCF7, DMSO Control for DRB, Rep1, H3K27ac, ChIP
- GSM8556958 MCF7, DMSO Control for DRB, Rep2, H3K27ac, ChIP
- GSM8556959 MCF7, DMSO Control for DRB, Pol II, ChIP
- GSM8556960 MCF7, DMSO Control for TRP, Rep1, ERalpha, ChIP
- GSM8556961 MCF7, DMSO Control for TRP, Rep2, ERalpha, ChIP
- GSM8556962 MCF7, DRB Treatment, Rep1, ERalpha, ChIP
- GSM8556963 MCF7, DRB Treatment, Rep2, ERalpha, ChIP
- GSM8556964 MCF7, DRB Treatment, Rep1, Flag, RRGG_mt, ChIP
- GSM8556965 MCF7, DRB Treatment, Rep2, Flag, RRGG_mt, ChIP
- GSM8556966 MCF7, DRB Treatment, Rep1, H3K27ac, ChIP
- GSM8556967 MCF7, DRB Treatment, Rep2, H3K27ac, ChIP
- GSM8556968 MCF7, DRB Treatment, Pol II, ChIP
- GSM8556969 MCF7, TRP Treatment, Rep1, ERalpha, ChIP
- GSM8556970 MCF7, TRP Treatment, Rep2, ERalpha, ChIP
- GSM8556971 MCF7, scramble RNA, ERalpha, ChIP
- GSM8556972 MCF7, exosc3 knockdown, ERalpha, ChIP
- GSM9006070 MCF7, scramble RNA, Rep2, ERalpha, ChIP
- GSM9006071 MCF7, exosc3 knockdown, Rep2, ERalpha, ChIP
- GSE68359 Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome 197 samples shares receptor-alpha, estrogen, binding
- GSE277183 RNA Polymerase II coordinates histone deacetylation at active promoters 158 samples shares polymerase, promoters
- GSE220316 Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability [ChIP-seq] 64 samples shares polymerase, pausing
- GSE223052 TFIIIC and MYCN link the three-dimensional chromatin structure of promoters to transcription termination of stalled RNA polymerase (ChIPseq CnR) 32 samples shares polymerase, promoters
- GSE316977 Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription [CUT&Tag] 16 samples shares polymerase, binding
- GSE294087 NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization 15 samples shares polymerase, binding
- GSE234640 KMT2D regulates Fanconi anemia pathway genes through regulating promoters/enhances upon glucose deprivation (CHIPseq) 14 samples shares promoters, enhances
- GSE241284 Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters 74 samples shares promoters, pausing
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.