Predictive modeling of chromatin features underlying replication timing
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 146 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
- 146 samples: 48 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
- KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transitionCell reports · 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 GSE216475_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 PRJNA893672 and SRA study SRP534197. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 96 samples.
How we read this: 48 replicated groups read from 146 sample titles; they account for 96 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.
- GSM6674471 Form_H2BK5ac_rep1 Form_H2BK5ac
- GSM6674472 Form_H2BK5ac_rep2 Form_H2BK5ac
- GSM6674473 Form_H3K27ac_rep1 Form_H3K27ac
- GSM6674474 Form_H3K27ac_rep2 Form_H3K27ac
- GSM6674475 Form_H3K27m3_rep1 Form_H3K27m3
- GSM6674476 Form_H3K27m3_rep2 Form_H3K27m3
- GSM6674477 Form_H3K36m1_rep1 Form_H3K36m1
- GSM6674478 Form_H3K36m1_rep2 Form_H3K36m1
- GSM6674479 Form_H3K36m2_rep1 Form_H3K36m2
- GSM6674480 Form_H3K36m2_rep2 Form_H3K36m2
- GSM6674481 Form_H3K4m2_rep1 Form_H3K4m2
- GSM6674482 Form_H3K4m2_rep2 Form_H3K4m2
- GSM6674483 Form_H3K4m3_rep1 Form_H3K4m3
- GSM6674484 Form_H3K4m3_rep2 Form_H3K4m3
- GSM6674485 Form_H3K9ac_rep1 Form_H3K9ac
- GSM6674486 Form_H3K9ac_rep2 Form_H3K9ac
- GSM6674487 Form_H3K9m3_rep1 Form_H3K9m3
- GSM6674488 Form_H3K9m3_rep2 Form_H3K9m3
- GSM6674489 Form_H4K20m1_rep1 Form_H4K20m1
- GSM6674490 Form_H4K20m1_rep2 Form_H4K20m1
- GSM6674491 Form_H4K8ac_rep1 Form_H4K8ac
- GSM6674492 Form_H4K8ac_rep2 Form_H4K8ac
- GSM6674493 Form_Rad21_rep1 Form_Rad21
- GSM6674494 Form_Rad21_rep2 Form_Rad21
- GSM6674495 Form_RNApolS2-5p_rep1 Form_RNApolS2-5p
- GSM6674496 Form_RNApolS2-5p_rep2 Form_RNApolS2-5p
- GSM6674497 Naive_H2BK5ac_rep1 Naive_H2BK5ac
- GSM6674498 Naive_H2BK5ac_rep2 Naive_H2BK5ac
- GSM6674499 Naive_H3K27ac_rep1 Naive_H3K27ac
- GSM6674500 Naive_H3K27ac_rep2 Naive_H3K27ac
- GSM6674501 Naive_H3K27m3_rep1 Naive_H3K27m3
- GSM6674502 Naive_H3K27m3_rep2 Naive_H3K27m3
- GSM6674503 Naive_H3K36m1_rep1 Naive_H3K36m1
- GSM6674504 Naive_H3K36m1_rep2 Naive_H3K36m1
- GSM6674505 Naive_H3K36m2_rep1 Naive_H3K36m2
- GSM6674506 Naive_H3K36m2_rep2 Naive_H3K36m2
- GSM6674507 Naive_H3K4m2_rep1 Naive_H3K4m2
- GSM6674508 Naive_H3K4m2_rep2 Naive_H3K4m2
- GSM6674509 Naive_H3K4m3_rep1 Naive_H3K4m3
- GSM6674510 Naive_H3K4m3_rep2 Naive_H3K4m3
+ 106 more — browse all 146 samples with per-sample file links →
- GSE262791 LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos 468 samples shares replication, timing
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares chromatin, modeling
- GSE239470 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling 74 samples shares chromatin, modeling
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares chromatin, modeling
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares chromatin, modeling
- GSE274493 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag] 46 samples shares chromatin, modeling
- GSE301108 Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome 45 samples shares chromatin, modeling
- GSE263333 Spatial-Mux-seq: Multiplexed spatial mapping of chromatin features, transcriptome, and proteins at tissue scale 12 samples shares chromatin, features
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.