 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 12, 2023 |
| Title |
Effects of Rift Valley fever virus infection on gene expression and alternative splicing in HEK 293 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Rift Valley fever virus (RVFV) is an important human and livestock pathogen. To better understand the molecular virology and mechanisms of pathogenesis in human HEK293 cells during RVFV MP-12 strain infection, we used high-throughput mRNA sequencing technology to identify and analyze differentially expressed genes and mRNA splicing patterns triggered by infection or by expression of RVFV nucleocapsid protein. Here we supply the results of our RNA-seq analysis of RVFV-infected cells and cells transfected with RVFV nucleocapsid protein expressing plasmids. Some of the results were published in: "Transcriptome profiling in Rift Valley fever virus infected cells reveals modified transcriptional and alternative splicing programs" by Katherine E Havranek, Luke Adam White, Jean-Marc Lanchy, J Stephen Lodmell. PLoS One. 2019 May 28;14(5):e0217497. PMID: 31136639 PMCID: PMC6538246.
|
| |
|
| Overall design |
To investigate the impact of Rift Valley Fever Virus (RVFV) infection on human gene expression and alternative splicing patterns, we infected HEK cells with RVFV MP12 strain and harvested total RNA two days post-infection. The transcript expression levels and alternative splicing events were measured by the analysis of 150-bp Illumina sequencing paired-reads of the purified polydenylated RNAs. We also analyzed, using the same Illumina sequencing technique, the impact heterologous expression of the viral RNA-binding N protein on host gene expression levels and alternative splicing events. The HEK293 cells used in that experiment were transfected with a viral N protein expression plasmid and the total RNA was harvested two days after the transfection and the purified polydenylated RNAs were processed for Illumina sequencing.
|
| |
|
| Contributor(s) |
Havranek KE, White LA, Lanchy J, Lodmell JS |
| Citation(s) |
31136639 |
| Submission date |
Sep 07, 2023 |
| Last update date |
Dec 12, 2023 |
| Contact name |
J Stephen Lodmell |
| E-mail(s) |
stephen.lodmell@mso.umt.edu
|
| Phone |
406 243-6393
|
| Organization name |
The University of Montana
|
| Department |
Biological Sciences
|
| Lab |
Lodmell
|
| Street address |
32 campus drive
|
| City |
Missoula |
| State/province |
MT |
| ZIP/Postal code |
59812 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (9)
|
| GSM7765966 |
HEK293 cells, Mock infection, day 2, replicate 1 |
| GSM7765967 |
HEK293 cells, Mock infection, day 2, replicate 2 |
| GSM7765968 |
HEK293 cells, Mock infection, day 2, replicate 3 |
| GSM7765969 |
HEK293 cells, RVFV N protein expression, day 2, replicate 1 |
| GSM7765970 |
HEK293 cells, RVFV N protein expression, day 2, replicate 2 |
| GSM7765971 |
HEK293 cells, RVFV N protein expression, day 2, replicate 3 |
| GSM7765972 |
HEK293 cells, RVFV infection, day 2, replicate 1 |
| GSM7765973 |
HEK293 cells, RVFV infection, day 2, replicate 2 |
| GSM7765974 |
HEK293 cells, RVFV infection, day 2, replicate 3 |
|
| Relations |
| BioProject |
PRJNA1013925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE242551_A3SS.miso_summary.txt.gz |
305.8 Kb |
(ftp)(http) |
TXT |
| GSE242551_A5SS.miso_summary.txt.gz |
217.7 Kb |
(ftp)(http) |
TXT |
| GSE242551_MP_12_vs_Mock.miso_bf.filtered.xlsx |
243.9 Kb |
(ftp)(http) |
XLSX |
| GSE242551_MP_12vsMock.DEG.fasta.gz |
15.9 Mb |
(ftp)(http) |
FASTA |
| GSE242551_MP_12vsMock.DEG.txt.gz |
946.4 Kb |
(ftp)(http) |
TXT |
| GSE242551_MXE.miso_summary.txt.gz |
210.9 Kb |
(ftp)(http) |
TXT |
| GSE242551_N_vs_MP_12.miso_bf.filtered.xlsx |
260.4 Kb |
(ftp)(http) |
XLSX |
| GSE242551_N_vs_Mock.miso_bf.filtered.xlsx |
107.5 Kb |
(ftp)(http) |
XLSX |
| GSE242551_NvsMP_12.DEG.fasta.gz |
15.5 Mb |
(ftp)(http) |
FASTA |
| GSE242551_NvsMP_12.DEG.txt.gz |
926.4 Kb |
(ftp)(http) |
TXT |
| GSE242551_NvsMock.DEG.fasta.gz |
8.1 Mb |
(ftp)(http) |
FASTA |
| GSE242551_NvsMock.DEG.txt.gz |
422.2 Kb |
(ftp)(http) |
TXT |
| GSE242551_RI.miso_summary.txt.gz |
161.8 Kb |
(ftp)(http) |
TXT |
| GSE242551_SE.miso_summary.txt.gz |
1006.4 Kb |
(ftp)(http) |
TXT |
| GSE242551_fpkm.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE242551_readcount.txt.gz |
616.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...