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Series GSE46254 Query DataSets for GSE46254
Status Public on Dec 01, 2013
Title Detection of small RNAs generated during early infection of human HEK 293 cells by the alphavirus Sindbis virus
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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.
 
Overall design 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
 
Contributor(s) Donaszi-Ivanov A, Mohorianu I, Dalmay T, Powell P
Citation(s) 24391886
Submission date Apr 22, 2013
Last update date May 15, 2019
Contact name Irina Mohorianu
E-mail(s) irina.mohorianu@paediatrics.ox.ac.uk
Organization name University of Oxford
Department Medical Sciences Division
Lab Oxford Vaccine Group
Street address Headington
City Oxford
ZIP/Postal code OX3 7LE
Country United Kingdom
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (3)
GSM1127038 HEK 293 SINV 0hpi
GSM1127039 HEK 293 SINV 4hpi
GSM1127040 HEK 293 SINV 6hpi
Relations
BioProject PRJNA198469
SRA SRP021459

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46254_RAW.tar 40.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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