Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 103
Release date: Jan 20 2016
Last update date: Oct 18 2018
Access: Public
Diseases: Hepatitis C
Dataset link A broad RNA virus survey reveals dependence on host miRNAs and specific sequestration modulating the cellular transcriptome

Experimental Protocol


Several subseries of analyses were performed. For each sample, subseries to which it belongs are indicated. In the “Virus AGO-CLIP” subseries, AGO-CLIP was performed on cells infected with virus as indicated. Processed reads were aligned to the host genome (hg18 or BosTau7) and to the respective viral genome. The primary data of interest from this subseries concerns AGO binding to viral RNA, and is given as processed data file “Table S1”. In the “Virus AGO-CLIP: BVDV vs. Mock” subseries, AGO-CLIP was performed on four replicates each of BVDV and mock infected MDBK cells. CLIP reads aligned to BosTau7 were clustered, and differential analysis was performed on binding to each cluster. In addition, differential analysis of AGO bound miRNAs was performed. The associated data is given as processed data file “Table S3 and S4”. In the “AGO-CLIP: tinyLNA-17 vs. Mock” AGO-CLIP was performed on four replicates each of tinyLNA-17 and mock treated MDBK cells. CLIP reads aligned to BosTau7 were clustered, and differential analysis was performed on binding to each cluster. The associated data is given as processed data file “Table S5”. In the “RNA-seq: BVDV vs. Mock” subseries, mRNA-seq was performed on two replicates each of MDBK cells infected with different biotypes of BVDV or with miR-17 seed site mutant BVDV. The latter (incl. mock controls) were trans-complemented with the corresponding mutated miR-17. Differential gene expression analysis was performed between selected conditions. The associated data is given as processed data file “Table S6”.

Repositories


GEO

GSE76967

ArrayExpress

E-GEOD-76967

ENA

SRP068577

BioProject

PRJNA309153

Download


Contact


Troels Scheel
Troels K H Scheel