Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 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
- 13 samples: 5 conditions, mostly in triplicateGroups 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
- Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNANature chemistry · 2024
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 GSE257561_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 PRJNA1080212 and SRA study SRP491608. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 5 replicated groups read from 13 sample titles; they account for 13 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.
- GSM8108142 HeLa, DNMT1, DMSO, CUT&Tag, rep1 HeLa, DNMT1, DMSO, CUT&…
- GSM8108143 HeLa, DNMT1, DMSO, CUT&Tag, rep2 HeLa, DNMT1, DMSO, CUT&…
- GSM8108144 HeLa, DNMT1, BQQ4h, CUT&Tag, rep1 HeLa, DNMT1, BQQ4h, CUT…
- GSM8108145 HeLa, DNMT1, BQQ4h, CUT&Tag, rep2 HeLa, DNMT1, BQQ4h, CUT…
- GSM8108146 HeLa, DDX3X, CUT&Tag, rep1 HeLa, DDX3X, CUT&Tag,
- GSM8108147 HeLa, DDX3X, CUT&Tag, rep2 HeLa, DDX3X, CUT&Tag,
- GSM8108148 HeLa, DDX3X, CUT&Tag, rep3 HeLa, DDX3X, CUT&Tag,
- GSM8108149 HeLa, gammaH2AX, scrambled siRNA, CUT&Tag, rep1 HeLa, gammaH2AX, scramb…
- GSM8108150 HeLa, gammaH2AX, scrambled siRNA, CUT&Tag, rep2 HeLa, gammaH2AX, scramb…
- GSM8108151 HeLa, gammaH2AX, scrambled siRNA, CUT&Tag, rep3 HeLa, gammaH2AX, scramb…
- GSM8108152 HeLa, gammaH2AX, siDDX3X, CUT&Tag, rep1 HeLa, gammaH2AX, siDDX3…
- GSM8108153 HeLa, gammaH2AX, siDDX3X, CUT&Tag, rep2 HeLa, gammaH2AX, siDDX3…
- GSM8108154 HeLa, gammaH2AX, siDDX3X, CUT&Tag, rep3 HeLa, gammaH2AX, siDDX3…
- GSE293802 Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3’UTR isoform diversity 18 samples shares diversity, proteins, binding
- GSE287132 DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation 18 samples shares proteins, binding
- GSE100638 Large-scale tethering of RNA binding proteins discovers alternative splicing regulators 220 samples shares proteins, binding
- GSE290248 Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection 97 samples shares proteins, binding
- GSE290282 Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq] 92 samples shares proteins, binding
- GSE100637 Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [RIP-Seq] 48 samples shares proteins, binding
- GSE268946 RNA-binding proteins DND1 and NANOS3 coordinately suppress SOX4 in processing bodies for restricting the entry of germ cell lineage 36 samples shares proteins, binding
- GSE311641 Oncofetal RNA-binding proteins IGF2BP suppress innate immune signaling pathways in leukemia stem cells [RNA-seq] 32 samples shares proteins, binding
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.