CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding sites in HEK293 cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 9 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
- 9 samples: 9 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
- MCM8 interacts with DDX5 to promote R-loop resolutionThe EMBO journal · 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 GSE254352_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 PRJNA1070001 and SRA study SRP486314. 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 9 sample titles: 9 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.
- GSM8039440 Mcm8_WT_MEF_S9.6
- GSM8039441 Mcm8_KO_MEF_S9.6
- GSM8039442 MEF_No_antibody
- GSM8039443 shControl_MEF_S9.6
- GSM8039444 shDdx5_MEF_S9.6
- GSM8039445 HEK293_Control
- GSM8039446 HEK293_FLAG_MCM8
- GSM8039447 HEK293_S9.6
- GSM8039448 HEK293_RNH1
- 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 hek293, mcm8, cut, tag, mcm8-binding, knockout, r-loops
- GSE249799 scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells 46 samples shares cut, tag
- GSE236218 Profiling R loop using S9.6 antibody coupled cut&tag 121 samples shares cut, tag
- GSE286290 Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [CUT&RUN] 81 samples shares cut
- GSE172296 A myeloid maturation program initiated by nucleotide depletion during S phase [Cut & Run] 47 samples shares cut
- GSE303627 MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia [CUT&Run] 46 samples shares cut
- GSE287346 MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species [CUT&Run] 33 samples shares cut
- GSE266386 Suppressing Aberrant Hedgehog Pathway and Overcoming Resistance to Smoothened Antagonists via Targeting Super-enhancer-driven Transcriptional Dependencies [ChIP-seq] 14 samples shares tag
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.