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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 13, 2024 |
| Title |
Viral and host network analysis of the human cytomegalovirus transcriptome in latency |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To investigate HCMV (and human host) gene expression profile during latency and reactivation, we infected THP-1 cells with the wildtype HCMV-TB40E or with recombinant viruses that cannot establish latency (UL138stop) or cannot reactivate (UL135stop).
After the establishment of viral latency, we treated cells with TPA to induce cellular differentiation and viral reactivation. We then performed gene expression profiling analysis using data obtained from RNA-seq over a timecourse of undifferentiated and differentiated cells
that are infected with each virus. Uninfected cells are included as a control for gene expression changes that are virally induced.
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| Overall design |
Temporal gene expression profiling analysis of RNA-Seq data for THP1 cells infected with HCMV wildtype or recombinant viruses
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| |
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| Contributor(s) |
Collins-McMillen D, de Oliveira Pessoa D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 07, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
Felicia Dare Goodrum |
| E-mail(s) |
fgoodrum@email.arizona
|
| Phone |
5206267468
|
| Organization name |
University of Arizona
|
| Department |
Immunobiology
|
| Lab |
Goodrum
|
| Street address |
1657 E Helen St
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85719 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (143)
|
| GSM8254813 |
THP1, uninfected, undifferentiated, day1, rep1 |
| GSM8254814 |
THP1, uninfected, undifferentiated, day3, rep1 |
| GSM8254815 |
THP1, uninfected, undifferentiated, day5, rep1 |
| GSM8254816 |
THP1, uninfected, undifferentiated, day5.5, rep1 |
| GSM8254817 |
THP1, uninfected, differentiated, day5.5, rep1 |
| GSM8254818 |
THP1, uninfected, undifferentiated, day6, rep1 |
| GSM8254819 |
THP1, uninfected, differentiated, day6, rep1 |
| GSM8254820 |
THP1, uninfected, undifferentiated, day8, rep1 |
| GSM8254821 |
THP1, uninfected, differentiated, day8, rep1 |
| GSM8254822 |
THP1, WTvirus, undifferentiated, day1, rep1 |
| GSM8254823 |
THP1, WTvirus, undifferentiated, day3, rep1 |
| GSM8254824 |
THP1, WTvirus, undifferentiated, day5, rep1 |
| GSM8254825 |
THP1, WTvirus, undifferentiated, day5.5, rep1 |
| GSM8254826 |
THP1, WTvirus, differentiated, day5.5, rep1 |
| GSM8254827 |
THP1, WTvirus, undifferentiated, day6, rep1 |
| GSM8254828 |
THP1, WTvirus, differentiated, day6, rep1 |
| GSM8254829 |
THP1, WTvirus, undifferentiated, day8, rep1 |
| GSM8254830 |
THP1, WTvirus, differentiated, day8, rep1 |
| GSM8254831 |
THP1, UL135stopvirus, undifferentiated, day1, rep1 |
| GSM8254832 |
THP1, UL135stopvirus, undifferentiated, day3, rep1 |
| GSM8254833 |
THP1, UL135stopvirus, undifferentiated, day5, rep1 |
| GSM8254834 |
THP1, UL135stopvirus, undifferentiated, day5.5, rep1 |
| GSM8254835 |
THP1, UL135stopvirus, differentiated, day5.5, rep1 |
| GSM8254836 |
THP1, UL135stopvirus, undifferentiated, day6, rep1 |
| GSM8254837 |
THP1, UL135stopvirus, differentiated, day6, rep1 |
| GSM8254838 |
THP1, UL135stopvirus, undifferentiated, day8, rep1 |
| GSM8254839 |
THP1, UL135stopvirus, differentiated, day8, rep1 |
| GSM8254840 |
THP1, UL138stopvirus, undifferentiated, day1, rep1 |
| GSM8254841 |
THP1, UL138stopvirus, undifferentiated, day3, rep1 |
| GSM8254842 |
THP1, UL138stopvirus, undifferentiated, day5, rep1 |
| GSM8254843 |
THP1, UL138stopvirus, undifferentiated, day5.5, rep1 |
| GSM8254844 |
THP1, UL138stopvirus, differentiated, day5.5, rep1 |
| GSM8254845 |
THP1, UL138stopvirus, undifferentiated, day6, rep1 |
| GSM8254846 |
THP1, UL138stopvirus, differentiated, day6, rep1 |
| GSM8254847 |
THP1, UL138stopvirus, undifferentiated, day8, rep1 |
| GSM8254848 |
THP1, UL138stopvirus, differentiated, day8, rep1 |
| GSM8254849 |
THP1, uninfected, undifferentiated, day1, rep2 |
| GSM8254850 |
THP1, uninfected, undifferentiated, day3, rep2 |
| GSM8254851 |
THP1, uninfected, undifferentiated, day5, rep2 |
| GSM8254852 |
THP1, uninfected, undifferentiated, day5.5, rep2 |
| GSM8254853 |
THP1, uninfected, differentiated, day5.5, rep2 |
| GSM8254854 |
THP1, uninfected, undifferentiated, day6, rep2 |
| GSM8254855 |
THP1, uninfected, differentiated, day6, rep2 |
| GSM8254856 |
THP1, uninfected, undifferentiated, day8, rep2 |
| GSM8254857 |
THP1, uninfected, differentiated, day8, rep2 |
| GSM8254858 |
THP1, WTvirus, undifferentiated, day1, rep2 |
| GSM8254859 |
THP1, WTvirus, undifferentiated, day3, rep2 |
| GSM8254860 |
THP1, WTvirus, undifferentiated, day5, rep2 |
| GSM8254861 |
THP1, WTvirus, undifferentiated, day5.5, rep2 |
| GSM8254862 |
THP1, WTvirus, differentiated, day5.5, rep2 |
| GSM8254863 |
THP1, WTvirus, undifferentiated, day6, rep2 |
| GSM8254864 |
THP1, WTvirus, differentiated, day6, rep2 |
| GSM8254865 |
THP1, WTvirus, undifferentiated, day8, rep2 |
| GSM8254866 |
THP1, WTvirus, differentiated, day8, rep2 |
| GSM8254867 |
THP1, UL135stopvirus, undifferentiated, day1, rep2 |
| GSM8254868 |
THP1, UL135stopvirus, undifferentiated, day3, rep2 |
| GSM8254869 |
THP1, UL135stopvirus, undifferentiated, day5, rep2 |
| GSM8254870 |
THP1, UL135stopvirus, undifferentiated, day5.5, rep2 |
| GSM8254871 |
THP1, UL135stopvirus, differentiated, day5.5, rep2 |
| GSM8254872 |
THP1, UL135stopvirus, undifferentiated, day6, rep2 |
| GSM8254873 |
THP1, UL135stopvirus, differentiated, day6, rep2 |
| GSM8254874 |
THP1, UL135stopvirus, undifferentiated, day8, rep2 |
| GSM8254875 |
THP1, UL135stopvirus, differentiated, day8, rep2 |
| GSM8254876 |
THP1, UL138stopvirus, undifferentiated, day1, rep2 |
| GSM8254877 |
THP1, UL138stopvirus, undifferentiated, day3, rep2 |
| GSM8254878 |
THP1, UL138stopvirus, undifferentiated, day5, rep2 |
| GSM8254879 |
THP1, UL138stopvirus, undifferentiated, day5.5, rep2 |
| GSM8254880 |
THP1, UL138stopvirus, differentiated, day5.5, rep2 |
| GSM8254881 |
THP1, UL138stopvirus, undifferentiated, day6, rep2 |
| GSM8254882 |
THP1, UL138stopvirus, differentiated, day6, rep2 |
| GSM8254883 |
THP1, UL138stopvirus, undifferentiated, day8, rep2 |
| GSM8254884 |
THP1, UL138stopvirus, differentiated, day8, rep2 |
| GSM8254885 |
THP1, uninfected, undifferentiated, day1, rep3 |
| GSM8254886 |
THP1, uninfected, undifferentiated, day3, rep3 |
| GSM8254887 |
THP1, uninfected, undifferentiated, day5, rep3 |
| GSM8254888 |
THP1, uninfected, undifferentiated, day5.5, rep3 |
| GSM8254889 |
THP1, uninfected, differentiated, day5.5, rep3 |
| GSM8254890 |
THP1, uninfected, undifferentiated, day6, rep3 |
| GSM8254891 |
THP1, uninfected, differentiated, day6, rep3 |
| GSM8254892 |
THP1, uninfected, undifferentiated, day8, rep3 |
| GSM8254893 |
THP1, uninfected, differentiated, day8, rep3 |
| GSM8254894 |
THP1, WTvirus, undifferentiated, day1, rep3 |
| GSM8254895 |
THP1, WTvirus, undifferentiated, day3, rep3 |
| GSM8254896 |
THP1, WTvirus, undifferentiated, day5, rep3 |
| GSM8254897 |
THP1, WTvirus, undifferentiated, day5.5, rep3 |
| GSM8254898 |
THP1, WTvirus, differentiated, day5.5, rep3 |
| GSM8254899 |
THP1, WTvirus, undifferentiated, day6, rep3 |
| GSM8254900 |
THP1, WTvirus, differentiated, day6, rep3 |
| GSM8254901 |
THP1, WTvirus, undifferentiated, day8, rep3 |
| GSM8254902 |
THP1, WTvirus, differentiated, day8, rep3 |
| GSM8254903 |
THP1, UL135stopvirus, undifferentiated, day1, rep3 |
| GSM8254904 |
THP1, UL135stopvirus, undifferentiated, day3, rep3 |
| GSM8254905 |
THP1, UL135stopvirus, undifferentiated, day5, rep3 |
| GSM8254906 |
THP1, UL135stopvirus, undifferentiated, day5.5, rep3 |
| GSM8254907 |
THP1, UL135stopvirus, differentiated, day5.5, rep3 |
| GSM8254908 |
THP1, UL135stopvirus, undifferentiated, day6, rep3 |
| GSM8254909 |
THP1, UL135stopvirus, differentiated, day6, rep3 |
| GSM8254910 |
THP1, UL135stopvirus, undifferentiated, day8, rep3 |
| GSM8254911 |
THP1, UL135stopvirus, differentiated, day8, rep3 |
| GSM8254912 |
THP1, UL138stopvirus, undifferentiated, day1, rep3 |
| GSM8254913 |
THP1, UL138stopvirus, undifferentiated, day3, rep3 |
| GSM8254914 |
THP1, UL138stopvirus, undifferentiated, day5, rep3 |
| GSM8254915 |
THP1, UL138stopvirus, undifferentiated, day5.5, rep3 |
| GSM8254916 |
THP1, UL138stopvirus, differentiated, day5.5, rep3 |
| GSM8254917 |
THP1, UL138stopvirus, undifferentiated, day6, rep3 |
| GSM8254918 |
THP1, UL138stopvirus, differentiated, day6, rep3 |
| GSM8254919 |
THP1, UL138stopvirus, differentiated, day8, rep3 |
| GSM8254920 |
THP1, uninfected, undifferentiated, day1, rep4 |
| GSM8254921 |
THP1, uninfected, undifferentiated, day3, rep4 |
| GSM8254922 |
THP1, uninfected, undifferentiated, day5, rep4 |
| GSM8254923 |
THP1, uninfected, undifferentiated, day5.5, rep4 |
| GSM8254924 |
THP1, uninfected, differentiated, day5.5, rep4 |
| GSM8254925 |
THP1, uninfected, undifferentiated, day6, rep4 |
| GSM8254926 |
THP1, uninfected, differentiated, day6, rep4 |
| GSM8254927 |
THP1, uninfected, undifferentiated, day8, rep4 |
| GSM8254928 |
THP1, uninfected, differentiated, day8, rep4 |
| GSM8254929 |
THP1, WTvirus, undifferentiated, day1, rep4 |
| GSM8254930 |
THP1, WTvirus, undifferentiated, day3, rep4 |
| GSM8254931 |
THP1, WTvirus, undifferentiated, day5, rep4 |
| GSM8254932 |
THP1, WTvirus, undifferentiated, day5.5, rep4 |
| GSM8254933 |
THP1, WTvirus, differentiated, day5.5, rep4 |
| GSM8254934 |
THP1, WTvirus, undifferentiated, day6, rep4 |
| GSM8254935 |
THP1, WTvirus, differentiated, day6, rep4 |
| GSM8254936 |
THP1, WTvirus, undifferentiated, day8, rep4 |
| GSM8254937 |
THP1, WTvirus, differentiated, day8, rep4 |
| GSM8254938 |
THP1, UL135stopvirus, undifferentiated, day1, rep4 |
| GSM8254939 |
THP1, UL135stopvirus, undifferentiated, day3, rep4 |
| GSM8254940 |
THP1, UL135stopvirus, undifferentiated, day5, rep4 |
| GSM8254941 |
THP1, UL135stopvirus, undifferentiated, day5.5, rep4 |
| GSM8254942 |
THP1, UL135stopvirus, differentiated, day5.5, rep4 |
| GSM8254943 |
THP1, UL135stopvirus, undifferentiated, day6, rep4 |
| GSM8254944 |
THP1, UL135stopvirus, differentiated, day6, rep4 |
| GSM8254945 |
THP1, UL135stopvirus, undifferentiated, day8, rep4 |
| GSM8254946 |
THP1, UL135stopvirus, differentiated, day8, rep4 |
| GSM8254947 |
THP1, UL138stopvirus, undifferentiated, day1, rep4 |
| GSM8254948 |
THP1, UL138stopvirus, undifferentiated, day3, rep4 |
| GSM8254949 |
THP1, UL138stopvirus, undifferentiated, day5, rep4 |
| GSM8254950 |
THP1, UL138stopvirus, undifferentiated, day5.5, rep4 |
| GSM8254951 |
THP1, UL138stopvirus, differentiated, day5.5, rep4 |
| GSM8254952 |
THP1, UL138stopvirus, undifferentiated, day6, rep4 |
| GSM8254953 |
THP1, UL138stopvirus, differentiated, day6, rep4 |
| GSM8254954 |
THP1, UL138stopvirus, undifferentiated, day8, rep4 |
| GSM8254955 |
THP1, UL138stopvirus, differentiated, day8, rep4 |
|
| Relations |
| BioProject |
PRJNA1108523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE266854_mock_wt_ul138_ul135_normalized_data.xlsx |
31.1 Mb |
(ftp)(http) |
XLSX |
| GSE266854_mock_wt_ul138_ul135_processed_sample_data.xlsx |
14.8 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
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