“Zipper” Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 10 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
- A tunable CTD grammar governs the spatial programming of the transcription cycleNature communications · 2026
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 GSE313488_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 PRJNA1356534 and SRA study SRP639976. 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 10 sample titles: 10 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.
- GSM9368860 HEK293T_CTD0_1rep
- GSM9368861 HEK293T_CTD0_2rep
- GSM9368862 HEK293T_CTD17_1rep
- GSM9368863 HEK293T_CTD17_2rep
- GSM9368864 HEK293T_Mix_S7E_sp_1rep
- GSM9368865 HEK293T_Mix_S7E_sp_2rep
- GSM9368866 HEK293T_Mix_T4E_sp_1rep
- GSM9368867 HEK293T_Mix_T4E_sp_2rep
- GSM9368868 HEK293T_Swapped_1rep
- GSM9368869 HEK293T_Swapped_2rep
- GSE287535 FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation 225 samples shares ctd, polymerase
- GSE284519 TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination [ChIP-seq] 93 samples shares transcription, chip-seq
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares transcription, chip-seq
- GSE335058 Evolutionary guided transcription factor design programs novel T cell states [ChIP-Seq] 66 samples shares transcription, chip-seq
- GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 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.