Decoding a combinatorial RNA polymerase II CTD grammar that specifies protein-coding gene transcription and mRNA export
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
- 24 samples: 5 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.
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 GSE325942_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 PRJNA1442667 and SRA study SRP498454. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 9 as controls.
How we read this: 5 replicated groups read from 24 sample titles; they account for 12 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.
- GSM8174027 HEK293T, T4A, rep1 HEK293T, T4A,
- GSM8174028 HEK293T, T4A, rep2 HEK293T, T4A,
- GSM8174029 HEK293T,WT, rep1
- GSM8174030 HEK293T, WT, rep2
- GSM8722189 T4A_52x_1rep
- GSM8722190 T4A_52x_2rep
- GSM8722191 WT_52x_1rep
- GSM8722192 WT_52x_2rep
- GSM9095531 HEK293_Ssu72_rep1 HEK293_Ssu72
- GSM9095532 HEK293_Mut_rep1 HEK293_Mut
- GSM9095533 HEK293_Ssu72_rep2 HEK293_Ssu72
- GSM9095534 HEK293_Mut_rep2 HEK293_Mut
- GSM9095535 HEK293_Input
- GSM9588862 pThr4 ChIP-seq, SCP1 WT treatment, biological replicate 1 pThr4 ChIP-seq, SCP1 WT…
- GSM9588863 pThr4 ChIP-seq, SCP1 WT treatment, biological replicate 2 pThr4 ChIP-seq, SCP1 WT…
- GSM9588864 pThr4 ChIP-seq, SCP1 WT treatment, biological replicate 3 pThr4 ChIP-seq, SCP1 WT…
- GSM9588865 pThr4 ChIP-seq, SCP1 D96A mutant treatment, biological replicate 1 pThr4 ChIP-seq, SCP1 D9…
- GSM9588866 pThr4 ChIP-seq, SCP1 D96A mutant treatment, biological replicate 2 pThr4 ChIP-seq, SCP1 D9…
- GSM9588867 pThr4 ChIP-seq, SCP1 D96A mutant treatment, biological replicate 3 pThr4 ChIP-seq, SCP1 D9…
- GSM9588868 IgG ChIP-seq negative control
- GSM9589545 HEK 293, WT_52x_1rep
- GSM9589546 HEK 293, WT_52x_2rep
- GSM9589547 HEK 293, T4A_52x_1rep
- GSM9589548 HEK 293, T4A_52x_2rep
- GSE287535 FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation 225 samples shares ctd, polymerase
- GSE328457 Pooled combinatorial screening identifies transcription factor sets that drive hematopoietic progenitor-like cell fate 39 samples shares combinatorial, transcription
- GSE336415 ZFP36L2 orchestrates stress-adaptive plasticity in intestinal regeneration and colorectal cancer metastasis (ActDseq) 24 samples shares ctd
- GSE314310 Cardiopedia-Ligand: a Ligand Stimulation Atlas for Cardiac Function and Transcriptional Response 468 samples shares transcription
- GSE303576 Rb-driven transcription limits its tumour suppressive effects in breast cancer 279 samples shares transcription
- GSE22098 Whole blood transcriptional profiles of patients with active tuberculosis (TB) and other inflammatory and infectious diseases 274 samples shares transcription
- GSE303478 Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome 217 samples shares transcription
- GSE271676 Spatial Transcriptional Landscape of Human Heart Failure 178 samples shares transcription
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.