3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [Cut&Tag]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 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
- Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcriptionNature communications · 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 GSE273972_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 PRJNA1144390 and SRA study SRP524241. 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 12 sample titles: 12 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.
- GSM8440910 MLg_H3K4me3_CaT_Ctr
- GSM8440911 MLg_H3K4me3_CaT_Mir9-LOF
- GSM8440912 MLg_H3K27ac_CaT_Ctr
- GSM8440913 MLg_H3K27ac_CaT_Mir9-LOF
- GSM8440914 MLE-12_H3K4me3_CaT_Ctr
- GSM8440915 MLE-12_H3K4me3_CaT_Mir9-LOF
- GSM8440916 MLE-12_H3K27ac_CaT_Ctr
- GSM8440917 MLE-12_H3K27ac_CaT_Mir9-LOF
- GSM8440918 MLg_Ctr_G4_CaT_r1
- GSM8440919 MLg_Mir9LOF_G4_CaT_r1
- GSM8440920 MLE-12_Ctr_G4_CaT_r1
- GSM8440921 MLE-12_Mir9LOF_G4_CaT
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription, nuclear
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares organization
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription
- GSE294521 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG] 34 samples shares transcription
- GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 samples shares transcription
- GSE324864 HP1B and H3K9me3 Regulate Olfactory Receptor Choice and 2 Transcriptional Identity [ChIP-seq] 28 samples shares transcription
- GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 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.