GEO series
DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions
GSE51334
Homo sapiens (human)
Other
993 samples
Submitted 2014/11/20
Platform GPL5648Platform GPL5668Platform GPL14965Platform GPL9973Platform GPL15656Platform GPL5729Platform GPL5646Platform GPL5666Platform GPL11620Platform GPL8840Platform GPL9052Platform GPL9115Platform GPL11154Platform GPL13112Platform GPL5669Platform GPL15651Platform GPL9250Platform GPL9156Platform GPL10999Platform GPL15436Platform GPL5649Platform GPL15225Platform GPL9185Platform GPL5644Platform GPL5667
At a glance
human · 993 samples
- Organism
- Homo sapiens (human)
- Samples
- 993 samples: 356 distinct titles, 37 of them repeatedGroups 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.
Summary (written by the submitters)
Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements.
Read the full summary ↓
Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale.Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.
This dataset
Download · which file do I need?
Direct links to NCBI, 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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need.
3 · The original raw files
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE51334_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
Also filed as BioProject PRJNA267243. Searching any of these in the dataset finder brings you back here.
Study design
356 distinct titles, 37 of them repeated
Bernstein_HSMM_H3K4me ×3
Bernstein_NHLF_H3K4me ×3
Bernstein_K562_H3K4me ×3
Bernstein_H1-hESC_H3K4me ×3
Bernstein_HUVEC_H3K4me ×3
Bernstein_NHEK_H3K4me ×3
Bernstein_GM12878_H3K4me ×3
Embryonic Stem Cell LaminB1 ×2
+29 more
How we read this: Read from the first 400 of 993 sample titles: 356 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
- GSM220158 Tig3 human fibroblast cells, LaminB1 DamID, platform 1/8
- GSM220159 Tig3 human fibroblast cells, LaminB1 DamID, platform 2/8
- GSM220160 Tig3 human fibroblast cells, LaminB1 DamID, platform 3/8
- GSM220161 Tig3 human fibroblast cells, LaminB1 DamID, platform 4/8
- GSM220162 Tig3 human fibroblast cells, LaminB1 DamID, platform 5/8
- GSM220163 Tig3 human fibroblast cells, LaminB1 DamID, platform 6/8
- GSM220164 Tig3 human fibroblast cells, LaminB1 DamID, platform 7/8
- GSM220165 Tig3 human fibroblast cells, LaminB1 DamID, platform 8/8
- GSM220166 Tig3 human fibroblast cells, LaminB1 DamID, platform chr4
- GSM220167 Tig3 human fibroblast cells, Emerin DamID, platform chr4
- GSM288360 ES_Suz12
- GSM426758 Embryonic Stem Cell LaminB1 1
- GSM426759 Embryonic Stem Cell LaminB1 2
- GSM450272 Replication timing of 46C ESC
- GSM450273 Replication timing of D3 ESC
- GSM450274 Replication timing of TT2 ESC
- GSM450275 Replication timing of iPSC
- GSM450276 Replication timing of iPSC, 1D4
- GSM450277 Replication timing of iPSC, 2D4
- GSM450279 Replication timing of D3 EBM3
- GSM450280 Replication timing of EpiSC5, clone O
- GSM450281 Replication timing of EpiSC7
- GSM450282 Replication timing of D3 EBM6
- GSM450283 Replication timing of 46C NPC/ASd6
- GSM450284 Replication timing of TT2 NPC/ASd9
- GSM450285 Replication timing of D3 NPC/EBM9
- GSM450286 Replication timing of Gsc+Sox17-Mesoderm
- GSM450287 Replication timing of Gsc+Sox17+Endoderm
- GSM450288 Replication timing of partially-reprogrammed iPSC, 1A2
- GSM450289 Replication timing of partially-reprogrammed iPSC, 1B3
- GSM450290 Replication timing of partially-reprogrammed iPSC, V3
- GSM450291 Replication timing of MEF (female)
- GSM450292 Replication timing of MEF (male)
- GSM450293 Replication timing of J185a myoblast
- GSM500932 Replication timing of BG01 ESC
- GSM500933 Replication timing of BG02 ESC, replicate 1
- GSM500934 Replication timing of BG02 ESC, replicate 2
- GSM500935 Replication timing of H7 ESC
- GSM500936 Replication timing of H9 ESC
- GSM500937 Replication timing of iPS4, replicate 1
+ 953 more — browse all 993 samples with per-sample file links →
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Share this dataset
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.