|
| Status |
Public on Mar 07, 2022 |
| Title |
E1E2-4 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Transfected with E1E2 expressing plasmid
cell type: Embryomic kidney cells
|
| Treatment protocol |
Cells were transfected using lipofectamine reagent with either a plasmid expressing the HCV (genome 1a) envelope glycoprotein E1E2 or with an empty vector plasmid, pCDNA. Cells were incubated for 2 days following transfection prior to extraction
|
| Growth protocol |
HEK293T cells grown in Advanced DMEM supplemented with FBS, penstrep and L-glutamine, seeded onto a 6 well plate to achieve 50-60% confluency at point of transfection
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted usign Qiagen RNAeasy Plus kit. All of the extracted RNA was used as input for PolyA+ RNA purification using Dynabeads mRNA purification kit.
Library was produced according to Oxford Nanopore cDNA sequencing protocol SQK-PCS-109 and barcoding protocol SQK-PCB-109
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
rawcounts.csv
DiffExpGenes.csv
|
| Data processing |
Barcoding using Oxford Nanopore Guppy software (version 3.2.4)
Demultiplex and trimming of adapters and barcodes using Porechop (https://github.com/rrwick/Porechop)
Mapping to human genome (GCA_000001405.15) using Minimap2
Mapped reads were assigned to genomic features using featureCounts
Normalisation of raw read counts was performed using EdgeR “trimmed mean M-values (TMM)” method
Differential gene expression between E1E2 or pCDNA transfected cells was determined using the R package Limma, using the “voom” method with a cut off of p=0.05
|
| |
|
| Submission date |
Dec 15, 2020 |
| Last update date |
Mar 07, 2022 |
| Contact name |
William Anderson Paxton |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Liverpool
|
| Department |
IVES
|
| Street address |
8 West Derby Street, Ronald Ross Building
|
| City |
Liverpool |
| State/province |
England |
| ZIP/Postal code |
L69 7BE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE163239 |
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates with Stimulation of the Host Endoplasmic Reticulum Stress Pathway |
|
| Relations |
| BioSample |
SAMN17084460 |
| SRA |
SRX9686557 |
