|
| Status |
Public on Jul 12, 2024 |
| Title |
PaKiT03 NoV infected 48hpi |
| Sample type |
SRA |
| |
|
| Source name |
PaKiT03
|
| Organism |
Pteropus alecto |
| Characteristics |
cell line: PaKiT03
cell type: kidney cell
genotype: wildtype
treatment: infected with NoV
|
| Treatment protocol |
Cells were plated in 6 cm dishes the day before infection. Infection was done with following titer: PR8delNS1 MOI=1, NoV/NoV∆B2 10 copies of genomic RNA1 per cell, SINVGFP MOI=0.5. Cells infected with NoV∆B2 were cultured at 30℃ during infection. At defined time post infection cells were harvested and total RNAs were extracted by TRIzol reagent then used for further analysis.
|
| Growth protocol |
All cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed with PBS twice, TRIzol was then added to the cells, and total RNAs were extracted following the manufacturer's instructions.
Extracted total RNAs were used for the construction of small RNA libraries by the method that depends on the 5’ monophosphate of small RNAs as described previously with the TruSeq Small RNA Sample Preparation Kit of Illumina (San Diego, CA).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
3’-adapters were trimmed and sRNAs containing any N base or overwhelming 10% of total reads were removed. Trimmed reads were first mapped to genome of Pteropus Alecto with 0 mis match, mappable reads were futher aligned to miRNAs (pal22-), tRNAs, rRNAs, snRNAs, snoRNAs of Pteropus alecto. Reads unmapped to host genome were aligned to viral genome. Alignment was done by Bowtie 1.2.2. Reads mapped to positive and negative strands were used to define positive and negative vsRNAs separately. Characterization of vsRNAs were performed as previously described
|
| Data processing |
3’-adapters were trimmed and sRNAs containing any N base or overwhelming 10% of total reads were removed.
Trimmed reads were first mapped to genome of Pteropus Alecto with 0 mis match, mappable reads were futher aligned to miRNAs (pal22-), tRNAs, rRNAs, snRNAs, snoRNAs of Pteropus alecto.
Reads unmapped to host genome were aligned to viral genome.
Characterization of vsRNAs were performed as previously described.
Assembly: Pteropus alecto (GCA_000325575.1), hg38
Supplementary files format and content: *.viralreads.xls for all perfect mapped virus-derived small RNA reads in each library (unnormalized)
Supplementary files format and content: *.miRNAreads.xls for all perfect mapped miRNA reads in each library (unnormalized)
|
| |
|
| Submission date |
Apr 12, 2024 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Yang Li |
| E-mail(s) |
yangli15@fudan.edu.cn
|
| Organization name |
Fudan university
|
| Street address |
2005 Songhu Rd, Yangpu district
|
| City |
Shanghai |
| ZIP/Postal code |
201601 |
| Country |
China |
| |
|
| Platform ID |
GPL15898 |
| Series (1) |
| GSE221607 |
Increased viral tolerance mediates by antiviral RNA interference in bat cells |
|
| Relations |
| BioSample |
SAMN40945517 |
| SRA |
SRX24235650 |
