GEO series

Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication [ChIP-Seq]

GSE293195 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 46 samples Submitted 2025/10/27 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 46 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: Homo sapiens (human)
Samples: 46 samples: 46 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: Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replicationNature communications · 2025

Summary (written by the submitters)

Replication origins in human cells form clusters ranging from tens to hundreds of kilobases called initiation zones (IZs), typically located in intergenic regions between active genes. On a larger megabase scale, chromosomes replicate in a temporally defined replication timing (RT) pattern, where euchromatic regions replicate early, and heterochromatic regions replicate late.

Read the full summary ↓

Although the stochastic model of IZ firing with a temporally regulated limiting factor can explain RT formation, this limiting factor in human cells remains unclear. To investigate the relationship between IZ and RT, we mapped the temporal firing pattern of IZs and examined the genome-wide distributions of replication licensing and firing factors in human cells. We identified TRESLIN-MTBP as the key limiting firing factor for replication initiation. Its loading onto phosphorylated MCM2–7 double hexamer (MCM-DH) is controlled by the opposing phosphorylation events on MCM-DH by Dbf4-dependent kinase and RIF1-Protein Phosphatase 1, which ultimately determine IZs and establish RT.

Published in

Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication

Zhu X, Bektash A, Hatoyama Y et al. · Nature communications 2025 · PMID 41331242 · doi:10.1038/s41467-025-66278-7

This dataset

Open GSE293195 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE293195_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1243334 and SRA study SRP573880. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41331242) ↗

Study design

46 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 46 sample titles: 46 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.

Samples in this study

GSM8878437 ChIP control with untagged cells, Late-G1, Rep1 (Input)
GSM8878438 ChIP control with untagged cells, Late-G1, Rep1 (ChIP)
GSM8878439 ChIP control with untagged cells, Late-G1, Rep2 (Input)
GSM8878440 ChIP control with untagged cells, Late-G1, Rep2 (ChIP)
GSM8878441 MCM2-3xFLAG cells, Late-G1, Rep1 (Input)
GSM8878442 MCM2-3xFLAG cells, Late-G1, Rep1 (ChIP)
GSM8878443 MCM2-3xFLAG cells, Late-G1, Rep2 (Input)
GSM8878444 MCM2-3xFLAG cells, Late-G1, Rep2 (ChIP)
GSM8878445 MCM2-3xFLAG cells, Late-G1, pre-extracted (Input)
GSM8878446 MCM2-3xFLAG cells, Late-G1, pre-extracted (ChIP)
GSM8878447 3xFLAG-ORC1 cells, Late-G1 (Input)
GSM8878448 3xFLAG-ORC1 cells, Late-G1 (ChIP)
GSM8878449 3xFLAG-ORC2 cells, Late-G1 (Input)
GSM8878450 3xFLAG-ORC2 cells, Late-G1 (ChIP)
GSM8878451 MCM4-3xFLAG cells, Late-G1 (Input)
GSM8878452 MCM4-3xFLAG cells, Late-G1 (ChIP)
GSM8878453 MCM4-3xFLAG Bromo-RNAPol2 cells, Late-G1, DMSO (Input)
GSM8878454 MCM4-3xFLAG Bromo-RNAPol2 cells, Late-G1, DMSO (ChIP)
GSM8878455 MCM4-3xFLAG Bromo-RNAPol2 cells, Late-G1, AGB1 (Input)
GSM8878456 MCM4-3xFLAG Bromo-RNAPol2 cells, Late-G1, AGB1 (ChIP)
GSM8878457 3xFLAG-ORC1 RIF1-KO cells, Late-G1 (Input)
GSM8878458 3xFLAG-ORC1 RIF1-KO cells, Late-G1 (ChIP)
GSM8878459 MCM2-3xFLAG RIF1-KO cells, Late-G1 (Input)
GSM8878460 MCM2-3xFLAG RIF1-KO cells, Late-G1 (ChIP)
GSM8878461 MCM4-3xFLAG RIF1-KO cells, Late-G1 (Input)
GSM8878462 MCM4-3xFLAG RIF1-KO cells, Late-G1 (ChIP)
GSM8878463 3xFLAG-TRESLIN cells, Early-G1 (Input)
GSM8878464 3xFLAG-TRESLIN cells, Early-G1 (ChIP)
GSM8878465 3xFLAG-TRESLIN GINS4-mAID cells, Early-S, DMSO (Input)
GSM8878466 3xFLAG-TRESLIN GINS4-mAID cells, Early-S, DMSO (ChIP)
GSM8878467 3xFLAG-TRESLIN GINS4-mAID cells, Early-S, 5phIAA (Input)
GSM8878468 3xFLAG-TRESLIN GINS4-mAID cells, Early-S, 5phIAA (ChIP)
GSM8878469 MTBP-3xFLAG cells, Early-G1 (Input)
GSM8878470 MTBP-3xFLAG cells, Early-G1 (ChIP)
GSM8878471 MTBP-3xFLAG CDC45-mAID cells, Early-S, DMSO (Input)
GSM8878472 MTBP-3xFLAG CDC45-mAID cells, Early-S, DMSO (ChIP)
GSM8878473 MTBP-3xFLAG CDC45-mAID cells, Early-S, 5phIAA (Input)
GSM8878474 MTBP-3xFLAG CDC45-mAID cells, Early-S, 5phIAA (ChIP)
GSM8878475 3xFLAG-TRESLIN RIF1-KO cells, Early-G1 (Input)
GSM8878476 3xFLAG-TRESLIN RIF1-KO cells, Early-G1 (ChIP)

+ 6 more — browse all 46 samples with per-sample file links →

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