Virus Dataset Detail

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Dataset Information
Accession GSE208078
Status 2023/6/20
Title The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (RNA-seq II)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Part 1: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) inducibly expressing ICP22 or ICP27 (doxycycline-induced) were analyzed for gene expression and read-through transcription by RNA-seq (total RNA). This experiment was performed in parallel to the corresponding OMNI-ATACseq libraries in replicate wells. ICP22 or ICP27 expression was induced for 24 h prior to other treatments or harvest, respectively. ICP22 expressing cells were additionally treated with KCl (200 mM) or control for 2 h prior to harvest. Part 2: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) doxycycline-inducibly expressing an artificial miRNA against SSRP1 (two separate cell lines expressing different amiRNAs) were mock, HSV-1 strain F wild type or US1 deletion mutant infected to analyze gene expression and read-through transcription. This experiment was performed in parallel to the corresponding OMNI-ATACseq libraries in replicate wells. Expression of amiRNAs was induced for 72 h prior to infection. Cells were inoculated for 1 h and then incubated for another 8 h. The experiment was conducted with PAA (350 ug/ml) treatment, which was added after the inoculum was removed, and doxycycline where indicated.
Samples
GSM ID Sample info Characteristics Description
GSM6336814 HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, 200mM KCl for 2h, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: 5ug/ml doxycycline for 24h, 200mM KCl for 2h ICP22_dox_KCl_rep1;ICP22/27 OE, salt stress
GSM6336815 HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, 200mM KCl for 2h, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: 5ug/ml doxycycline for 24h, 200mM KCl for 2h ICP22_dox_KCl_rep2;ICP22/27 OE, salt stress
GSM6336816 HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, no KCl, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: 5ug/ml doxycycline for 24h, no KCl ICP22_dox_rep1;ICP22/27 OE, salt stress
GSM6336817 HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, no KCl, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: 5ug/ml doxycycline for 24h, no KCl ICP22_dox_rep2;ICP22/27 OE, salt stress
GSM6336818 HFF-tert dox-inducible ICP22, no dox, 200mM KCl for 2h, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: no doxycycline, 200mM KCl for 2h ICP22_no_dox_KCl_rep1;ICP22/27 OE, salt stress
GSM6336819 HFF-tert dox-inducible ICP22, no dox, 200mM KCl for 2h, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: no doxycycline, 200mM KCl for 2h ICP22_no_dox_KCl_rep2;ICP22/27 OE, salt stress
GSM6336820 HFF-tert dox-inducible ICP22, no dox, no KCl, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: no doxycycline, no KCl ICP22_no_dox_rep1;ICP22/27 OE, salt stress
GSM6336821 HFF-tert dox-inducible ICP22, no dox, no KCl, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP22 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: no doxycycline, no KCl ICP22_no_dox_rep2;ICP22/27 OE, salt stress
GSM6336822 HFF-tert dox-inducible ICP27, 5ug/ml dox for 24h, no KCl, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP27 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: 5ug/ml doxycycline for 24h, no KCl ICP27_dox_rep1;ICP22/27 OE, salt stress
GSM6336823 HFF-tert dox-inducible ICP27, 5ug/ml dox for 24h, no KCl, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP27 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: 5ug/ml doxycycline for 24h, no KCl ICP27_dox_rep2;ICP22/27 OE, salt stress
GSM6336824 HFF-tert dox-inducible ICP27, no dox, no KCl, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP27 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: no doxycycline, no KCl ICP27_no_dox_rep1;ICP22/27 OE, salt stress
GSM6336825 HFF-tert dox-inducible ICP27, no dox, no KCl, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible ICP27 cassette and rtTA3;time post_infection: N/A;infection: N/A;treatment: no doxycycline, no KCl ICP27_no_dox_rep2;ICP22/27 OE, salt stress
GSM6336826 HFF-tert dox-inducible amiRNA1 Mock, +PAA, 8 hpi, Mock, no dox, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: Mock, +PAA, 8 hpi;infection: Mock;treatment: no doxycycline, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment) Mock_minus_dox_rep1;SSRP1 KD
GSM6336827 HFF-tert dox-inducible amiRNA2 Mock, +PAA, 8 hpi, Mock, no dox, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: Mock, +PAA, 8 hpi;infection: Mock;treatment: no doxycycline, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment) Mock_minus_dox_rep2;SSRP1 KD
GSM6336828 HFF-tert dox-inducible amiRNA1 Mock, +PAA, 8 hpi, Mock, 5ug/ml dox for 24 h, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: Mock, +PAA, 8 hpi;infection: Mock;treatment: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA;supplemented upon removal of inoculum (8h treatment) Mock_plus_dox_rep1;SSRP1 KD
GSM6336829 HFF-tert dox-inducible amiRNA2 Mock, +PAA, 8 hpi, Mock, 5ug/ml dox for 24 h, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: Mock, +PAA, 8 hpi;infection: Mock;treatment: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA;supplemented upon removal of inoculum (8h treatment) Mock_plus_dox_rep2;SSRP1 KD
GSM6336830 HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, no dox, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi,+PAA infection: HSV-1, strain F;treatment: no doxycycline, 350 ug/ml PAA;supplemented upon removal of inoculum (8h treatment) Wt_minus_dox_rep1;SSRP1 KD
GSM6336831 HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, no dox, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA infection: HSV-1, strain F;treatment: no doxycycline, 350 ug/ml PAA;supplemented upon removal of inoculum (8h treatment) Wt_minus_dox_rep2;SSRP1 KD
GSM6336832 HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, 5ug/ml dox for 24 h, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA infection: HSV-1, strain F;treatment: 5ug/ml doxycycline for 24 h, 350 ug/ml;PAA supplemented upon removal of inoculum (8h treatment) Wt_plus_dox_rep1;SSRP1 KD
GSM6336833 HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, 5ug/ml dox for 24 h, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA infection: HSV-1, strain F;treatment: 5ug/ml doxycycline for 24 h, 350 ug/ml;PAA supplemented upon removal of inoculum (8h treatment) Wt_plus_dox_rep2;SSRP1 KD
GSM6336834 HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, US1 deleted, no dox, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA;infection: HSV-1, strain F, US1 deleted;treatment: no doxycycline, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment) ICP22_minus_dox_rep1;SSRP1 KD
GSM6336835 HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, US1 deleted, no dox, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA;infection: HSV-1, strain F, US1 deleted;treatment: no doxycycline, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment) ICP22_minus_dox_rep2;SSRP1 KD
GSM6336836 HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, US1 deleted, 5ug/ml dox for 24 h, rep1 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA;infection: HSV-1, strain F, US1 deleted;treatment: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment) ICP22_plus_dox_rep1;SSRP1 KD
GSM6336837 HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, US1 deleted, 5ug/ml dox for 24 h, rep2 tissue: foreskin;cell line: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line;transduction: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1);time post_infection: 8 hpi, +PAA;infection: HSV-1, strain F, US1 deleted;treatment: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment) ICP22_plus_dox_rep1;SSRP1 KD
Platform GPL18573  : Illumina NextSeq 500 (Homo sapiens)
Literature 37524699  
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xCell Plot
* p<0.05 ** p<0.01