Profiling R loop using S9.6 antibody coupled cut&tag
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 121 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
- Mus musculus (mouse)
- Samples
- 121 samples
- 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 GSE236218_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 PRJNA989270 and SRA study SRP446668. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 121 more — browse all 121 samples with per-sample file links →
- GSE99521 YY1 is a structural regulator of enhancer-promoter loops 47 samples shares loop
- GSE293376 Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus 38 samples shares antibody
- GSE289625 RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [RNAseq] 28 samples shares loop
- GSE254764 Genome-wide mapping of native G-loops in living cells 28 samples shares loop
- GSE273256 IgE plasma cells differentially regulate antibody secretion, ER stress and tissue-specific longevity relative to other isotypes 18 samples shares antibody
- GSE254352 CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding sites in HEK293 cells 9 samples shares loop
- GSE240230 CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding site in HEK293 cells 6 samples shares loop
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.