Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 23 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
- 23 samples: 23 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
- Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organizationNucleic acids research · 2025
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 GSE243534_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 PRJNA1018867 and SRA study SRP461653. 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 23 sample titles: 23 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.
- GSM7785442 RBFox2_ActD
- GSM7785443 RBFox2_NT
- GSM7785446 Input
- GSM7790584 K562_bio1_tech1_siNC
- GSM7790585 K562_bio1_tech1_siRBFox2
- GSM7790586 K562_bio2_tech1-siNC
- GSM7790587 K562_bio2_tech1-siRBFox2
- GSM7790588 K562_bio3_tech1-siNC
- GSM7790589 K562_bio3_tech1-siRBFox2
- GSM7790590 K562_bio4_tech1_siNC
- GSM7790591 K562_bio4_tech1_siRBFox2
- GSM7790600 C2C12_bio1_ActD
- GSM7790601 C2C12_bio1_NT
- GSM7790604 C2C12_bio2_ActD
- GSM7790605 C2C12_bio2_NT
- GSM7790607 C2C12_bio3_ActD
- GSM7790608 C2C12_bio3_NT
- GSM7790611 C2C12_bio4_ActD
- GSM7790612 C2C12_bio4_NT
- GSM7790615 C2C12_bio5_ActD
- GSM7790616 C2C12_bio5_NT
- GSM7790619 C2C12_bio6_ActD
- GSM7790620 C2C12_bio6_NT
- GSE269226 Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [RNA-Seq] 20 samples shares tad
- GSE96981 Multilineage communication regulates human liver bud self-organization from pluripotency II 741 samples shares organization
- GSE49417 The conserved organization of the human and mouse transcriptomes 64 samples shares organization
- GSE238001 Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells 18 samples shares organization
- GSE311199 Integrative spatial profiling of 3D genome organization and gene expression in complex tissue 15 samples shares organization
- GSE249331 Differences in mitotic chromosome organization between cell types and species 15 samples shares organization
- GSE266161 RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing 13 samples shares enrichment
- GSE246346 Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP 11 samples shares organization
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.