3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 25 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
- 25 samples: 25 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
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 GSE244952_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 PRJNA1026484 and SRA study SRP465380. 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 25 sample titles: 25 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.
- GSM7832497 01MLg_Mir9_ChIRP
- GSM7832498 02MLg_Inp_ChIRP
- GSM7832499 01MLg_K4m3_HICHIP_Ctr
- GSM7832500 02MLg_K4m3_HICHIP_Tgfb
- GSM7832501 03MLg_K4m3_HICHIP_Tgfb_antiMir9
- GSM7832502 04MLg_K4m3_HICHIP_Mir9_LOF
- GSM7832503 01MLg_RNAs_riZero_Ctr
- GSM7832504 02MLg_RNAs_riZero_Mir9_LOF
- GSM7832505 03MLg_RNAs_riZero_Tgfb
- GSM7832506 04MLg_RNAs_riZero_Tgfb_Mir9_LOF
- 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
- GSM8440922 x01Mlg_Ctr_H3K4me3_ChIP
- GSM8440923 x02Mlg_TGFB_H3K4me3_ChIP
- GSM8440924 x03Mlg_TGFB_Mir9LOF_H3K4me3_ChIP
- 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
- GSE284504 Transcriptional profiling of brain from a zQ175 KI mouse model of Huntington's disease 335 samples shares transcription
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares transcription
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares transcription
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares transcription
- GSE229815 Transcriptional profiling of 12 month striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Msh2 heterozygous or homozygous conditional knockout mice [Msh2_12mon] 138 samples shares transcription
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares organization
- GSE225576 An atlas of the aging mouse transcriptome and proteome reveals the features of age-related post-transcriptional dysregulation 128 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.