|
| Status |
Public on Jan 01, 2017 |
| Title |
Tick20 |
| Sample type |
SRA |
| |
|
| Source name |
cultured cells
|
| Organism |
Ixodes ricinus |
| Characteristics |
time point: Day7
agent: Tick-borne encephalitis virus infected
|
| Treatment protocol |
Tick cells were infected with Louping ill virus (LI3/1 strain) or tick-borne encephalitis virus (Neudorfl H2J strain), and cells/supernatant sampled at 7 post-infection. Mock infected (uninfected) cells/supernatant were sampled at day 0.
|
| Growth protocol |
IRE/CTVM20 cells were maintained in a 1:1 mixture of L-15 (Leibovitz) medium and L-15B medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen), according to the manufacturer's protocol, and further purified using the Rneasy Mini kit (Qiagen). Ribosomal RNA was depleted using Terminator Exonuclease (Epicentre).
Double stranded cDNA synthesis using Roche cDNA Synthesis System. Illumina library construction using NexteraXT kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalling with CASAVA v1.8
Alignment using BowTie2
Identification of splice junctions using TopHat2
Estimation of gene abundance and differential gene expression using Cufflinks.
Normalization of biological replicates using Cuffmerge
Estimation of abundance across normalized samples using Cuffquant.
Identification of differentially expressed genes using Cuffdiff.
Genome_build: JCVI_ISG_i3_1.0
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for all Samples
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Ellis |
| Organization name |
Animal and Plant Health Agency
|
| Street address |
APHA Weybridge
|
| City |
Addlestone |
| ZIP/Postal code |
KT15 3NB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21340 |
| Series (1) |
| GSE85300 |
Tick-borne Pathogens Induce Differential Expression of Genes Promoting Cell Survival and Host Resistence in Ixodes ricinus Cells |
|
| Relations |
| BioSample |
SAMN05521487 |
| SRA |
SRX2007409 |
