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Sample GSM4955661 Query DataSets for GSM4955661
Status Public on Dec 07, 2020
Title RatPyV2 Parotid
Sample type SRA
 
Source name Tissue
Organism Rattus norvegicus
Characteristics tissue: Parotid gland
infection status: RatPyV2 infected
treatment: RnaseR+, ribodepleted RNA
Treatment protocol Samples 3, HEK-293 cells were transfected with a recircularized MCV-HF genome for 5 days and harvested for RNA extraction.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
Submission date Dec 03, 2020
Last update date Dec 08, 2020
Contact name Bizunesh Abere
E-mail(s) baa103@pitt.edu
Phone 4126237733
Organization name Hillman Cancer Center
Department Cancer Virology Program
Lab Chang and Moore
Street address 5117 Centre Ave, Research Pav. Suite 1.8
City Pittsburgh
State/province PENNSYLVANIA
ZIP/Postal code 15213
Country USA
 
Platform ID GPL22396
Series (1)
GSE162627 Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network
Relations
BioSample SAMN16989390
SRA SRX9628534

Supplementary file Size Download File type/resource
GSM4955661_RatParotidvsRatPyV2outfile.txt.gz 658 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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