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| Status |
Public on Oct 17, 2012 |
| Title |
Footprints from cells infected with HCMV for 5hr, pretreated with cycloheximide |
| Sample type |
SRA |
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| Source name |
Human fibroblasts infected with HCMV, cycloheximide, 5hr
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| Organism |
Human betaherpesvirus 5 |
| Characteristics |
strain: Merlin
cell type: HCMV-infected human foreskin fibroblasts
drug pre-treatment: cycloheximide
infection duration: 5hr
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with 0.5% Triton, and the lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using the acid:phenol extraction method.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
fp_chx_05hr_s1
Ribosome-protected mRNA.
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| Data processing |
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_chx_05hr_s1_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_chx_05hr_s1_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2
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| Submission date |
Oct 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Noam Ginossar |
| Organization name |
UCSF
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| Street address |
1700 4th street
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| City |
San Francisco |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL16185 |
| Series (1) |
| GSE41605 |
Decoding human cytomegalovirus using ribosome profiling |
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| Relations |
| SRA |
SRX201524 |
| BioSample |
SAMN01795915 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1020234_fp_chx_05hr_s1_merlin.align.unique.p_offset.5_prime.merged.minus.wig.gz |
150.9 Kb |
(ftp)(http) |
WIG |
| GSM1020234_fp_chx_05hr_s1_merlin.align.unique.p_offset.5_prime.merged.plus.wig.gz |
76.7 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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