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Series GSE156618

Query DataSets for GSE156618

Status

Public on May 19, 2021

Title

Replication timing data for six human cell lines under aphidicolin treatment (t0) and after release (N+1)

Organism

Experiment type

Other

Summary

DNA replication is very well orchestrated in mammalian cells due to a tight regulation of the temporal order of replication origin activation, known as the replication timing program. The replication timing of a given replication domain is very robust and well conserved in each cell type. Upon low replication stress, the slowing of replication forks induces delayed replication of some fragile regions leading to DNA damage and genetic instability. Except for these fragile regions, the direct impact of low replication stress on the replication timing in different cellular backgrounds has not been explored in detail. Here we analysed DNA replication timing across the whole genome in a panel of human cell lines in the presence of low replication stress. We demonstrate that low replication stress induced by aphidicolin has a stronger impact on the replication timing of cancer cells than non-tumour cells. Strikingly, we unveiled an enrichment of specific replication domains undergoing a switch from late to early replication in some cancer cells. We found that advances in replication timing correlate with heterochromatin regions poorly sensitive to DNA damage signalling while being subject to an increase of chromatin accessibility in response to aphidicolin. Finally, our data indicate that, following release from replication stress conditions, replication timing advances can be inherited by the next cellular generation, suggesting a new mechanism by which some cancer cells would adapt to cellular or environmental stress.

Overall design

The 6 human cell lines were treated with aphidicolin 0.2µM or DMSO during adapted duration. T0 correspond to the replication timing of cells under the treatment and N+1 correspond to the replication timing of cells released from the drug during appropriate duration.
Biological replicates for each conditions (37 samples)

Contributor(s)

Citation(s)

https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22094959

Submission date

Aug 21, 2020

Last update date

Jul 15, 2021

Contact name

Valérie Bergoglio

E-mail(s)

valerie.bergoglio@inserm.fr

Phone

0582741655

Organization name

INSERM UMR1037

Lab

CRCT

Street address

2 avenue Hubert Curien

City

Toulouse cedex 1

ZIP/Postal code

31037

Country

France

Platforms (1)

Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version)

Samples (37)

More...

GSM4734938	HCT116 replication timing in DMSO condition - Rep1
GSM4734939	HCT116 replication timing in APH condition - Rep1
GSM4734940	HCT116 replication timing in DMSO condition - Rep2

GSM4734941	HCT116 replication timing in APH condition - Rep2
GSM4734942	K562 replication timing in DMSO condition - Rep1
GSM4734943	K562 replication timing in APH condition - Rep1
GSM4734944	K562 replication timing in DMSO condition - Rep2
GSM4734945	K562 replication timing in APH condition - Rep2
GSM4734946	MRC5N replication timing in DMSO condition - Rep1
GSM4734947	MRC5N replication timing in APH condition - Rep1
GSM4734948	MRC5N replication timing in DMSO condition - Rep2
GSM4734949	MRC5N replication timing in APH condition - Rep2
GSM4734950	RKO replication timing in DMSO condition - Rep1
GSM4734951	RKO replication timing in APH condition - Rep1
GSM4734952	RKO replication timing in DMSO condition - Rep2
GSM4734953	RKO replication timing in APH condition - Rep2
GSM4734954	RPE-1 replication timing in DMSO condition - Rep1
GSM4734955	RPE-1 replication timing in APH condition - Rep1
GSM4734956	RPE-1 replication timing in DMSO condition - Rep2
GSM4734957	RPE-1 replication timing in APH condition - Rep2
GSM4734958	U2OS replication timing in DMSO condition - Rep1
GSM4734959	U2OS replication timing in APH condition - Rep1
GSM4734960	U2OS replication timing in DMSO condition - Rep2
GSM4734961	U2OS replication timing in APH condition - Rep2
GSM4734962	HCT116 daughter cells (N+1) replication timing in APH condition - Rep1
GSM4734963	HCT116 daughter cells (N+1) replication timing in APH condition - Rep2
GSM4734964	K562 daughter cells (N+1) replication timing in APH condition - Rep1
GSM4734965	K562 daughter cells (N+1) replication timing in APH condition - Rep2
GSM4734966	MRC5N daughter cells (N+1) replication timing in APH condition - Rep1
GSM4734967	RKO daughter cells (N+1) replication timing in DMSO condition - Rep1
GSM4734968	RKO daughter cells (N+1) replication timing in APH condition - Rep1
GSM4734969	RKO daughter cells (N+1) replication timing in DMSO condition - Rep2
GSM4734970	RKO daughter cells (N+1) replication timing in APH condition - Rep2
GSM4734971	RPE-1 daughter cells (N+1) replication timing in APH condition - Rep1
GSM4734972	RPE-1 daughter cells (N+1) replication timing in APH condition - Rep2
GSM4734973	U2OS daughter cells (N+1) replication timing in APH condition - Rep1
GSM4734974	U2OS daughter cells (N+1) replication timing in APH condition - Rep2

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE156618_HCT116_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_HCT116_DMSO_vs_APH_N+1.bed.gz	274 b	(ftp)(http)	BED
GSE156618_HCT116_DMSO_vs_APH_t0.bed.gz	1.2 Kb	(ftp)(http)	BED
GSE156618_HCT116_N+1_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_HCT116_t0_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_K562_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_K562_DMSO_vs_APH_N+1.bed.gz		(ftp)(http)	BED
GSE156618_K562_DMSO_vs_APH_t0.bed.gz	883 b	(ftp)(http)	BED
GSE156618_K562_N+1_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_K562_t0_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_MRC5N_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_MRC5N_DMSO_vs_APH_N+1.bed.gz	253 b	(ftp)(http)	BED
GSE156618_MRC5N_DMSO_vs_APH_t0.bed.gz	746 b	(ftp)(http)	BED
GSE156618_MRC5N_N+1_APH_log_ratio.txt.gz	3.5 Mb	(ftp)(http)	TXT
GSE156618_MRC5N_t0_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RAW.tar	1.9 Gb	(http)(custom)	TAR (of TXT)
GSE156618_RKO_DMSO_vs_APH_N+1.bed.gz	401 b	(ftp)(http)	BED
GSE156618_RKO_DMSO_vs_APH_t0.bed.gz	788 b	(ftp)(http)	BED
GSE156618_RKO_N+1_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RKO_N+1_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RKO_t0_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RKO_t0_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RPE-1_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RPE-1_DMSO_vs_APH_N+1.bed.gz	108 b	(ftp)(http)	BED
GSE156618_RPE-1_DMSO_vs_APH_t0.bed.gz	630 b	(ftp)(http)	BED
GSE156618_RPE-1_N+1_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_RPE-1_t0_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_U2OS_DMSO_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_U2OS_DMSO_vs_APH_N+1.bed.gz	154 b	(ftp)(http)	BED
GSE156618_U2OS_DMSO_vs_APH_t0.bed.gz	964 b	(ftp)(http)	BED
GSE156618_U2OS_N+1_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
GSE156618_U2OS_t0_APH_log_ratio.txt.gz	4.8 Mb	(ftp)(http)	TXT
Processed data are available on Series record

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