GSE33584
GSE GEOHigh-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
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Summary
Small RNA deep sequencing analysis was conducted on primary human fibroblasts infected with human cytomegalovirus (HCMV). HCMV-encoded miRNAs accumulated to ~20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identification of novel HCMV miRNAs. Through crosslinking and immunoprecipitation of Argonaute-bound RNAs from infected cells, followed by high-throughput sequencing (Ago CLIP-seq), we obtained direct evidence for incorporation of all HCMV miRNAs into the endogenous host silencing machinery. Additionally, significant upregulation was observed during infection for a host miRNA cluster containing miR-96, miR-182 and miR-183. We also identified novel non-miRNA forms of virus-derived smRNAs, revealing greater complexity within the smRNA population during HCMV infection.
Overall Design
High-throughput profiling of smRNAs, Ago1-, and Ago2-associated miRNAs from HCMV-infected fibroblast cells. Wild-type HCMV Towne (Genbank FJ616285.1) was used for these studies.
Analysis (2 steps)
View Data Processing- Adapter-trimmed sequencing libraries were mapped against an index composed of both the human (UCSC hg19, http://genome.ucsc.edu) and HCMV Towne (Genbank FJ616285.1) genomes, using Bowtie software (version 0.12.7, with parameters -k 1 -m 10 -l 25 --best).
- Custom Perl scripts were used to overlap mapped coordinates with smRNA annotations, which were obtained from miRBase 16.0 (http://www.mirbase.org) and the UCSC Table Browser.
Supplementary Files (1)
Dataset Citations (1)
SRA Experiments (4) and Runs (4)
Total: 222 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR363673 | 4537120 | 145187840 | 70.47 | smRNA_mock_24h.fastq, SRR363673, SRR363673.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR363674 | 3494456 | 111822592 | 55.34 | smRNA_mock_72h.fastq, SRR363674, SRR363674.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR363675 | 4152077 | 132866464 | 56.15 | smRNA_infected_24h.fastq, SRR363675, SRR363675.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR363676 | 2530263 | 80968416 | 40.11 | smRNA_infected_72h.fastq, SRR363676, SRR363676.sralite | SRA |
Linked Publications (1)
Data Files (9)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | smRNA_infected_24h.fastq | RNA-Seq | 56.1 MB | link | |||
| — | smRNA_infected_72h.fastq | RNA-Seq | 40.1 MB | link | |||
| — | smRNA_mock_24h.fastq | RNA-Seq | 70.5 MB | link | |||
| — | smRNA_mock_72h.fastq | RNA-Seq | 55.3 MB | link | |||
| — | SRR363673_GSM830250 | RNA-Seq | 70.0 MB | link | |||
| — | SRR363674_GSM830251 | RNA-Seq | 55.0 MB | link | |||
| — | SRR363675_GSM830252 | RNA-Seq | 56.0 MB | link | |||
| — | SRR363676 | RNA-Seq | 40.1 MB | link | |||
| — | SRR363676_GSM830253 | RNA-Seq | 40.0 MB | link |