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| Status |
Public on Dec 07, 2020 |
| Title |
MS-1 |
| Sample type |
SRA |
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| Source name |
MCC derived cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCC derived cell line
infection status: MCV positive
treatment: RnaseR+, ribodepleted RNA
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| Treatment protocol |
Samples 3, HEK-293 cells were transfected with a recircularized MCV-HF genome for 5 days and harvested for RNA extraction.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent (Invitrogen) was used to extract total RNA, according to the manufacturer’s instructions and treated with DnaseI (Ambion) to remove geomic DNA.
For RNA qulity control and circRNA library preparation, a total amount of 6 μg RNA per sample was used as input material. Ribosomal RNA was removed by rRNA probe andlinear RNA was removed by Rnase R (Lucigen). The CircRNA was interrupted randomly in adding fragmentation buffer.
Using the fragmented CircRNA as a template, the first strand was synthesized with a random hexamers of six bases, followed by the addition of buffer, dNTPs, RNase H and DNA polymerase I to synthesize the second strand of the cDNA, then the CircRNA was purified by AMPure XP beads. The cohesive ends of the DNA were repaired to blunt ends using T4 DNA polymerase and Klenow DNA polymerase, 3'-end plus A-tail and ligated to the sequencing adapter followed by selection of the size of the fragment with AMPure XP beads, afterwards, the second strand of cDNA containing U was degraded with USER enzyme. CircRNA library was amplified by PCR.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw FastQ files were trimmed with Trim Galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ using the following parameters -q 25, -e 0.1, and - length 50, and the quality control was performed with FastQC.
Backspliced splice junctions were identified and mapped using CIRI2 prediction algorithm
Genome_build: MCV (JF813003) and RatPyV2 (KX574453)
Supplementary_files_format_and_content: backsplice junctions identified exported as txt
CVG-1vsMCVoutfile.txt (no circRNA detected)
MS-1vsMCVoutfile.txt (no circRNA detected)
HEK-293-MCV-HFvs MCVoutfile.txt
RatParotidvsRatPyV2outfile.txt
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| Submission date |
Dec 03, 2020 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Bizunesh Abere |
| E-mail(s) |
baa103@pitt.edu
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| Phone |
4126237733
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| Organization name |
Hillman Cancer Center
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| Department |
Cancer Virology Program
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| Lab |
Chang and Moore
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| Street address |
5117 Centre Ave, Research Pav. Suite 1.8
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| City |
Pittsburgh |
| State/province |
PENNSYLVANIA |
| ZIP/Postal code |
15213 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE162627 |
Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network |
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| Relations |
| BioSample |
SAMN16989392 |
| SRA |
SRX9628532 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4955659_MS-1vsMCVoutfile.txt.gz |
144 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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