LDB1 regulates gene expression and chromatin structure in pluripotency and lineage differentiation [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: 6 conditions, mostly in duplicateGroups 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
- LDB1 regulates gene expression and chromatin structure in pluripotency and lineage differentiationbioRxiv : the preprint server for biology · 2025
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 GSE282374_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 PRJNA1188464 and SRA study SRP546363. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 of them. 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.
- GSM8642154 ESC_H3K27me3_WT_rep1 ESC_H3K27me3_WT
- GSM8642155 ESC_H3K27me3_WT_rep2 ESC_H3K27me3_WT
- GSM8642156 ESC_H3K27me3_KO_rep1 ESC_H3K27me3_KO
- GSM8642157 ESC_H3K27me3_KO_rep2 ESC_H3K27me3_KO
- GSM8642158 ESC_H3K4me3_WT_rep1 ESC_H3K4me3_WT
- GSM8642159 ESC_H3K4me3_WT_rep2 ESC_H3K4me3_WT
- GSM8642160 ESC_H3K4me3_KO_rep1 ESC_H3K4me3_KO
- GSM8642161 ESC_H3K4me3_KO_rep2 ESC_H3K4me3_KO
- GSM8642162 ESC_H3K27ac_WT_rep1 ESC_H3K27ac_WT
- GSM8642163 ESC_H3K27ac_WT_rep2 ESC_H3K27ac_WT
- GSM8642164 ESC_H3K27ac_KO_rep1 ESC_H3K27ac_KO
- GSM8642165 ESC_H3K27ac_KO_rep2 ESC_H3K27ac_KO
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares chromatin, structure
- GSE342312 T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics] 40 samples shares chromatin, lineage
- GSE272524 Chromatin-dependent motif syntax defines differentiation trajectories [ChIP-seq] 76 samples shares chromatin
- GSE306869 The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation 24 samples shares chromatin
- GSE204933 Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice 82 samples shares chromatin
- GSE255571 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag] 10 samples shares chromatin
- GSE294085 SIRT6 Overexpression Counteracts Chromatin Aging [ChIP-Seq] 74 samples shares chromatin
- GSE278416 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression 40 samples shares chromatin
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.