|
| Status |
Public on Mar 23, 2023 |
| Title |
17-CL1_shCTL_24hpi_1 |
| Sample type |
SRA |
| |
|
| Source name |
17-CL1 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 17-CL1
genotype: shCTL
treatment: Infected with mouse hepatitis virus
viral strain: MHV-S (ATCC_VR-766)
duration: 24 hours
|
| Treatment protocol |
Cells were infected with 10 M.O.I. of MHV for different timepoints
|
| Growth protocol |
Mouse 17-CL1 cells were cultured in DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The 17-CL1 cells were cultured at 37ºC and in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA from 17-CL1 shCTL and shTUT4/7 knowckdown cells were used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.
|
| |
|
| Submission date |
Apr 07, 2022 |
| Last update date |
Mar 23, 2023 |
| Contact name |
ANKIT GUPTA |
| E-mail(s) |
[email protected]
|
| Organization name |
NIEHS
|
| Department |
RDBL
|
| Street address |
TW 111 ALEXANDER DRIVE
|
| City |
DURHAM |
| ZIP/Postal code |
27713 |
| Country |
USA |
| |
|
| Platform ID |
GPL24973 |
| Series (2) |
| GSE200413 |
Role of TUT4 and TUT7 on the regulation of MHV poly(A) tail length and 3' end additions [17-CL1_Mutants] |
| GSE200416 |
Determination of MHV RNA poly(A) tail length and 3' end additions in infected 17-CL1 and NCTC cells |
|
| Relations |
| BioSample |
SAMN27404480 |
| SRA |
SRX14776271 |
