Genome instability Track Settings

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Genome instability (All R-loopBase Data tracks)

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All	*Cell Line*	BEAS-2B	COLO320-DM	COLO321-HSR	HCT116	HeLa	HepG2	lymphoblastoid	MCF10	MCF7	RPE1-hTERT	U2OS-DIvA	*Cell Line*	All
*Technology*													*Technology*
BLISS													BLISS
END-seq													END-seq
H2AX-ChIP-seq													H2AX-ChIP-seq
H2AX-CUT&Tag													H2AX-CUT&Tag
HS-Damage-seq													HS-Damage-seq

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	Cell Line^↓1	Technology^↓2	Strand^↓3	Track Name^↓4
full Configure	BEAS-2B	HS-Damage-seq	no	bigwig_21_BEAS-2B_control_HS-Damage-seq_rep1	Schema
full Configure	BEAS-2B	HS-Damage-seq	no	bigwig_20_BEAS-2B_control_HS-Damage-seq_rep1	Schema
full Configure	COLO320-DM	END-seq	minus	bigwig_6_COLO320-DM_control_END-seq_minus_rep1	Schema
full Configure	COLO320-DM	END-seq	plus	bigwig_6_COLO320-DM_control_END-seq_plus_rep1	Schema
full Configure	COLO321-HSR	END-seq	minus	bigwig_7_COLO321-HSR_control_END-seq_minus_rep1	Schema
full Configure	COLO321-HSR	END-seq	plus	bigwig_7_COLO321-HSR_control_END-seq_plus_rep1	Schema
full Configure	HCT116	BLISS	no	bigwig_23_HCT116_control_BLISS_rep2	Schema
full Configure	HCT116	BLISS	no	bigwig_22_HCT116_control_BLISS_rep1	Schema
full Configure	HeLa	END-seq	no	bigwig_5_HeLa_control_END-seq_rep2	Schema
full Configure	HeLa	END-seq	no	bigwig_4_HeLa_control_END-seq_rep1	Schema
full Configure	HeLa	H2AX-ChIP-seq	no	bigwig_11_HeLa_control_H2AX-ChIP-seq_rep1	Schema
full Configure	HepG2	H2AX-CUT&Tag	no	bigwig_15_HepG2_control_H2AX-CUT&Tag_rep1	Schema
full Configure	HepG2	H2AX-ChIP-seq	no	bigwig_12_HepG2_control_H2AX-ChIP-seq_rep1	Schema
full Configure	MCF10	END-seq	minus	bigwig_3_MCF10_control_END-seq_minus_rep1	Schema
full Configure	MCF10	END-seq	plus	bigwig_3_MCF10_control_END-seq_plus_rep1	Schema
full Configure	MCF7	BLISS	no	bigwig_24_MCF7_control_BLISS_rep1	Schema
full Configure	MCF7	BLISS	no	bigwig_25_MCF7_control_BLISS_rep1	Schema
full Configure	MCF7	H2AX-ChIP-seq	no	bigwig_13_MCF7_control_H2AX-ChIP-seq_rep1	Schema
full Configure	RPE1-hTERT	END-seq	no	bigwig_1_RPE1-hTERT_control_END-seq_rep1	Schema
full Configure	RPE1-hTERT	END-seq	no	bigwig_2_RPE1-hTERT_control_END-seq_rep1	Schema
full Configure	U2OS-DIvA	H2AX-CUT&Tag	no	bigwig_14_U2OS-DIvA_control_H2AX-CUT&Tag_rep1	Schema
full Configure	lymphoblastoid	H2AX-ChIP-seq	no	bigwig_10_lymphoblastoid_control_H2AX-ChIP-seq_rep2	Schema
full Configure	lymphoblastoid	H2AX-ChIP-seq	no	bigwig_9_lymphoblastoid_control_H2AX-ChIP-seq_rep1	Schema

Description

This track integrates genomic datasets related to DNA damage and genome instability, including END-seq, BLISS, H2AX ChIP-seq, and Damage-seq. END-seq and BLISS map DNA double-strand break (DSB) sites, H2AX ChIP-seq detects genomic regions associated with the DNA damage response, and Damage-seq maps DNA damage sites at high resolution. Together, these datasets provide complementary information for investigating the genomic distribution of DNA damage and instability and their potential association with R-loop formation.

Reference

Jiang Y, Mingard C, Huber SM, et al, Quantification and Mapping of Alkylation in the Human Genome Reveal Single Nucleotide Resolution Precursors of Mutational Signatures.. ACS Cent Sci. 2023 Mar 22;9(3):362-372. PMID: 36968528

Feng S, Liu K, Shang J, et al, Profound synthetic lethality between SMARCAL1 and FANCM.. Mol Cell. 2024 Dec 5;84(23):4522-4537. PMID: 39510066

Mosler T, Conte F, Longo GMC, et al, R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability.. Nat Commun. 2021 Dec 16;12(1):7314. PMID: 34916496

Hazan I, Monin J, Bouwman BAM, et al, Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51.. Cell Rep. 2019 Oct 15;29(3):560-572.e4. PMID: 31618627

Lyu X, Chastain M, Chai W, Genome-wide mapping and profiling of ?H2AX binding hotspots in response to different replication stress inducers.. BMC Genomics. 2019 Jul 12;20(1):579. PMID: 31299901

Jung H, Lee Y, Yu D, et al, Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition.. bioRxiv. 2024 Dec 5;84(23):4522-4537. PMID: 41357980

Zou F, Yao Z, Dong X, et al, DNA-PK-mediated CRTC2 phosphorylation promotes NHEJ and suppresses antitumor immunity via relocation to repair complexes.. Nat Commun. 2024 Dec 5;84(23):4522-4537. PMID: 42151152

Fu J, Wei Y, Yang Y, et al, Intranuclear paraspeckle-circular RNA TACC3 assembly forms RNA-DNA hybrids to facilitate MASH-related hepatocellular carcinoma growth in an m(6)A-dependent manner.. Cancer Commun (Lond). 2025 Nov;45(11):1583-1610. PMID: 41103024