|
| Status |
Public on Sep 16, 2016 |
| Title |
Cisplatin DNA Damage and Repair Maps of the Human Genome at Single-nucleotide Resolution |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Platinum chemotherapies induce damages in DNA that distort the helical structure. In human cells, these adducts are removed primarily by the Nucleotide Excision Repair pathway. In this study, we mapped both cisplatin and oxaliplatin induced damages and their repair at single nucleotide resolution across the human genome.
|
| |
|
| Overall design |
We performed Damage-seq to map 2 types of damages in two different human cell lines. The damages were cisplatin and oxaliplatin induced DNA adducts. The two cell lines were normal human skin fibroblasts NHF1 and the GM12878 human lymphoblastoid cells. As control, cisplatin damages were induced in genomic DNA from GM12878. For comparison to repair, XR-seq was performed for cisplatin and oxaliplatin treated GM12878 cells.
|
| |
|
| Contributor(s) |
Adar S, Hu J, Lieb JD, Sancar A |
| Citation(s) |
27688757 |
| |
| Submission date |
Jun 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sheera Adar |
| Organization name |
Hebrew University of Jerusalem
|
| Department |
Department of Microbiology and Molecular Genetics
|
| Lab |
Sheera Adar
|
| Street address |
Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem
|
| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
91120 |
| Country |
Israel |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (14)
|
|
| Relations |
| BioProject |
PRJNA324370 |
| SRA |
SRP076092 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE82213_HL64_merged_4nt_sorted_MINUS_NORM_fixedStep_25.bw |
128.6 Mb |
(ftp)(http) |
BW |
| GSE82213_HL64_merged_4nt_sorted_PLUS_NORM_fixedStep_25.bw |
131.2 Mb |
(ftp)(http) |
BW |
| GSE82213_HL64vitro_merged_sorted_MINUS_NORM_fixedStep_25.bw |
85.1 Mb |
(ftp)(http) |
BW |
| GSE82213_HL64vitro_merged_sorted_PLUS_NORM_fixedStep_25.bw |
86.5 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCPD_merged_4nt_sorted_MINUS_NORM_fixedStep_25.bw |
105.0 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCPD_merged_4nt_sorted_PLUS_NORM_fixedStep_25.bw |
107.0 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCPDvitro_merged_sorted_MINUS_NORM_fixedStep_25.bw |
97.2 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCPDvitro_merged_sorted_PLUS_NORM_fixedStep_25.bw |
97.3 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCisP_merged_4nt_sorted_MINUSNORM_fixedStep_25.bw |
99.6 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCisP_merged_4nt_sorted_PLUSNORM_fixedStep_25.bw |
101.0 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCisPvitro_merged_sorted_MINUSNORM_fixedStep_25.bw |
96.9 Mb |
(ftp)(http) |
BW |
| GSE82213_HLCisPvitro_merged_sorted_PLUSNORM_fixedStep_25.bw |
98.2 Mb |
(ftp)(http) |
BW |
| GSE82213_HLOxP_merged_sorted_MINUSNORM_fixedStep_25.bw |
72.7 Mb |
(ftp)(http) |
BW |
| GSE82213_HLOxP_merged_sorted_PLUSNORM_fixedStep_25.bw |
73.8 Mb |
(ftp)(http) |
BW |
| GSE82213_HLunD_merged_sorted_MINUSNORM_fixedStep_25.bw |
50.4 Mb |
(ftp)(http) |
BW |
| GSE82213_HLunD_merged_sorted_PLUSNORM_fixedStep_25.bw |
50.9 Mb |
(ftp)(http) |
BW |
| GSE82213_NHF164_merged_4nt_sorted_MINUS_NORM_fixedStep_25.bw |
99.7 Mb |
(ftp)(http) |
BW |
| GSE82213_NHF164_merged_4nt_sorted_PLUS_NORM_fixedStep_25.bw |
101.8 Mb |
(ftp)(http) |
BW |
| GSE82213_NHF1CPD_merged_4nt_sorted_MINUS_NORM_fixedStep_25.bw |
98.2 Mb |
(ftp)(http) |
BW |
| GSE82213_NHF1CPD_merged_4nt_sorted_PLUS_NORM_fixedStep_25.bw |
98.9 Mb |
(ftp)(http) |
BW |
| GSE82213_OXP_XR_Rep2_MINUS_UNIQUE_NORM_fixedStep_25.bw |
134.3 Mb |
(ftp)(http) |
BW |
| GSE82213_OXP_XR_Rep2_PLUS_UNIQUE_NORM_fixedStep_25.bw |
136.9 Mb |
(ftp)(http) |
BW |
| GSE82213_RAW.tar |
1.0 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
Less...
More...