|
| Status |
Public on May 24, 2018 |
| Title |
Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Uracil in DNA can be generated as a result of cytosine deamination or dUMP misincorporation. However, its distribution in the human genome is poorly understood, due to the lack of a sensitive detection method. Here we present “dU-seq”, a selective labeling and pull-down technology, to profile uracil in the human genome. dU-seq specifically labels uracil-containing DNA via an in vitro base excision repair reaction and identifies thousands of uracil peaks in the human genome.
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| Overall design |
dU-seq performed on three wild-type cell lines, one KO cell line and two 5-fluorodeoxyuridine treated cells; sample Titles with "biotin-dCTP" means in the dU-seq library preparation, the DNA labeling step utilized biotin-dCTP while other samples utilized biotin-dUTP; sample Titles with "5F" means 5-fluorodeoxyuridine treated cells.
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| Contributor(s) |
Shu X, Lu Z, Yi C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
zhike lu |
| E-mail(s) |
zhikelu@gmail.com
|
| Organization name |
University of Chicago
|
| Department |
department of chemistry
|
| Street address |
5801 South Ellis Avenue
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (1) |
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| Samples (54)
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| Relations |
| BioProject |
PRJNA387005 |
| SRA |
SRP107197 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99011_293TPD.uniq.peaks.bed.gz |
120.0 Kb |
(ftp)(http) |
BED |
| GSE99011_5F_293TPD.uniq.peaks.bed.gz |
92.0 Kb |
(ftp)(http) |
BED |
| GSE99011_5F_UNGKOPD.uniq.peaks.bed.gz |
536.9 Kb |
(ftp)(http) |
BED |
| GSE99011_K562PD.uniq.peaks.bed.gz |
15.2 Kb |
(ftp)(http) |
BED |
| GSE99011_R1.293TPDuniq.bed.gz |
107.1 Kb |
(ftp)(http) |
BED |
| GSE99011_R1.UNGKOPDuniq.bed.gz |
114.5 Kb |
(ftp)(http) |
BED |
| GSE99011_R2.293TPDuniq.bed.gz |
67.0 Kb |
(ftp)(http) |
BED |
| GSE99011_R2.UNGKOPDuniq.bed.gz |
19.5 Kb |
(ftp)(http) |
BED |
| GSE99011_R3.UNGKOPDuniq.bed.gz |
49.8 Kb |
(ftp)(http) |
BED |
| GSE99011_R4.UNGKOPDuniq.bed.gz |
67.7 Kb |
(ftp)(http) |
BED |
| GSE99011_biotin-dCTP_293TPD.uniq.peaks.bed.gz |
17.4 Kb |
(ftp)(http) |
BED |
| GSE99011_biotin-dCTP_K562PD.uniq.peaks.bed.gz |
35.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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