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| Status |
Public on Jul 19, 2018 |
| Title |
Relative accessability of HSV1 genomic DNA compared with its host cell (ATAC-seq) |
| Organisms |
Homo sapiens; Human alphaherpesvirus 1 strain KOS |
| Experiment type |
Other
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| Summary |
To compare the relative accessability of HSV1 DNA compared with its host DNA, we performed ATAC-seq analysis.
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| Overall design |
Cells were left uninfected; infected for 2, 4, or 6 hours; or infected for 6 hours in the presence of phosphonoacetic acid to prevent genome replication. ATAC-seq was performed as per standard published protocols.
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| Contributor(s) |
McSwiggen DT, Tjian R, Darzacq X |
| Citation(s) |
31038454 |
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| Submission date |
Jul 18, 2018 |
| Last update date |
May 29, 2019 |
| Contact name |
David Trombley McSwiggen |
| Organization name |
University of California Berkeley
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| Department |
Molecular and Cell Biology
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| Lab |
Tjian
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| Street address |
470 Li Ka Shing Center
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
97406 |
| Country |
USA |
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| Platforms (1) |
| GPL25348 |
Illumina HiSeq 2500 (Homo sapiens; Human alphaherpesvirus 1 strain KOS) |
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| Samples (15)
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| GSM3291176 |
HSV1 infected, 6hpi, pooled replicates |
| GSM3291177 |
HSV1 infected with PAA, 6hpi, pooled replicates |
| GSM3291178 |
U2OS Uninfected, Replicate 1 |
| GSM3291179 |
HSV1 infected, 2hpi, Replicate 1 |
| GSM3291180 |
HSV1 infected, 4hpi, Replicate 1 |
| GSM3291181 |
HSV1 infected, 6hpi, Replicate 1 |
| GSM3291182 |
HSV1 infected with PAA, 6hpi, Replicate 1 |
| GSM3291183 |
U2OS Uninfected, Replicate 2 |
| GSM3291184 |
HSV1 infected, 2hpi, Replicate 2 |
| GSM3291185 |
HSV1 infected, 4hpi, Replicate 2 |
| GSM3291186 |
HSV1 infected, 6hpi, Replicate 2 |
| GSM3291187 |
HSV1 infected with PAA, 6hpi, Replicate 2 |
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| Relations |
| BioProject |
PRJNA481773 |
| SRA |
SRP154375 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117335_RAW.tar |
6.2 Gb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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