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Series GSE116650 Query DataSets for GSE116650
Status Public on Oct 11, 2018
Title RIG-I and MDA5 fRIP during KSHV lytic reactivation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The RIG-I like receptors (RLRs) RIG-I and MDA5 are cytosolic RNA helicases best characterized as restriction factors for RNA viruses. However, evidence suggests RLRs participate in innate immune recognition of other pathogens, including DNA viruses. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human gammaherpesvirus and the etiological agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). We demonstrate that RIG-I and MDA5 restrict KSHV lytic reactivation in PEL. By performing fRIP-Seq, we define the in vivo RLR substrates and demonstrate that RIG-I and MDA5-mediated restriction is facilitated exclusively by the recognition of host-derived RNAs.
Overall design Inducible F-RIG-I and F-MDA5 BC-3 cells, as well as control BC-3 cells were treated with 1 μg/ml of doxycycline, 20ng/ml tetradecanoyl phorbol acetate and 0.1 mM sodium butyrate for 48 h. Flag fRIP was performed and RNA was submitted for high throughput sequencing.
Contributor(s) Zhao Y, Ye X
Citation(s) 30451863
Submission date Jul 05, 2018
Last update date Dec 23, 2018
Contact name Jeff Rathmell
Organization name Vanderbilt University Medical Center
Department PMI
Lab Jeff Rathmell Lab
Street address 1211 Medical Center Drive
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (8)
GSM3244862 F-RIG-I Input, replicate1
GSM3244863 F-MDA5 Input, replicate1
GSM3244864 F-RIG-I fRIP, replicate1
BioProject PRJNA479810
SRA SRP152218

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE116650_gene_exp.diff.txt.gz 9.0 Mb (ftp)(http) TXT
GSE116650_genes.count_tracking.txt.gz 1.2 Mb (ftp)(http) TXT
GSE116650_genes.fpkm_tracking.txt.gz 2.5 Mb (ftp)(http) TXT
GSE116650_genes.read_group_tracking.txt.gz 2.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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