CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cells [Cut & Tag]
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: 3 × RPE1_Pol2ser5_R1T vs 3 × RPE1_Pol2ser5_R2T vs 2 × RPE1_H3K4me1_R1T vs 2 × RPE1_H3K4me1_R2TGroups 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
- CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cellsbioRxiv : the preprint server for biology · 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 GSE318107_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 PRJNA1416661 and SRA study SRP671499. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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.
- GSM9486268 RPE1_H3K4me1_R1T1 RPE1_H3K4me1_R1T
- GSM9486269 RPE1_H3K4me1_R1T2 RPE1_H3K4me1_R1T
- GSM9486270 RPE1_H3K4me1_R2T1 RPE1_H3K4me1_R2T
- GSM9486271 RPE1_H3K4me1_R2T2 RPE1_H3K4me1_R2T
- GSM9486272 RPE1_Pol2ser5_R1T1 RPE1_Pol2ser5_R1T
- GSM9486273 RPE1_Pol2ser5_R1T2 RPE1_Pol2ser5_R1T
- GSM9486274 RPE1_Pol2ser5_R1T3 RPE1_Pol2ser5_R1T
- GSM9486275 RPE1_Pol2ser5_R2T1 RPE1_Pol2ser5_R2T
- GSM9486276 RPE1_Pol2ser5_R2T2 RPE1_Pol2ser5_R2T
- GSM9486277 RPE1_Pol2ser5_R2T3 RPE1_Pol2ser5_R2T
- GSE318018 CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cells 6 samples shares cad-c, nucleosome-resolution, repair-free, engineered, chromosome, proximity, nuclease, ligation
- GSE290620 Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [ATAC-seq] 25 samples shares engineered, nuclease
- GSE57283 Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases 108 samples shares engineered, nuclease
- GSE290621 Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [RNA-seq] 33 samples shares engineered, nuclease
- GSE267065 Transcriptome analysis and ribosome footprints in engineered chromosome 3 and chromosome 8 isogenic aneuploidy cell model. 9 samples shares engineered, chromosome
- GSE328352 Engineered amphiregulin promotes tissue healing via multiple mechanisms following acute injury 12 samples shares engineered
- GSE331444 Engineered heart tissues facilitate functional characterization of noncoding variants implicated in Hypertrophic and Dilated Cardiomyopathy [ATAC-seq] 6 samples shares engineered
- GSE281263 Identification of a novel PDC-E2 epitope in Primary Biliary Cholangitis and application for engineered Treg therapy 632 samples shares engineered
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.