E-GEOD-46254 - Detection of small RNAs generated during early infection of human HEK 293 cells by the alphavirus Sindbis virus

Released on 1 December 2013, last updated on 3 June 2014
Homo sapiens
Samples (3)
Protocols (3)
A time course of infection of the alphavirus Sindbis virus (SINV) was used to investigate the presence of viral specific vsRNA and the changes in miRNAs profiles in human embryonic kidney 293 cells (HEK293) by high throughput DNA sequencing. Deep sequencing of small RNAs early in SINV infection (4 and 6 hpi) showed low abundance (0.8%) of viral specific RNAs (vsRNAs) , with a random uniform distribution not typical of Dicer products, suggesting they arise from non-specific degradation. Sequencing showed little variation of cellular microRNAs (miRNAs) at 4 and 6 hpi compared to uninfected cells. Twelve miRNAs exhibiting some minor differential expression by sequencing, showed insignificant modulation by Northern blot analysis. RNA was isolated from mock infected and SINV inoculated HEK 293 cells at 4hpi and 6hpi cDNA libraries were generated for the small RNA (sRNA) content of the cells and sequenced using Illumina GA II, which yielded between 29.1M and 30.5M reads per sample
Experiment type
RNA-seq of non coding RNA 
Irina Mohorianu <i.mohorianu@uea.ac.uk>, Andras Donaszi-Ivanov, Penny Powell, Tamas Dalmay
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-46254.idf.txt
Sample and data relationshipE-GEOD-46254.sdrf.txt
Processed data (1)E-GEOD-46254.processed.1.zip