|
| Status |
Public on Apr 22, 2015 |
| Title |
221-12hpi |
| Sample type |
SRA |
| |
|
| Source name |
SL221 cell
|
| Organism |
Spodoptera litura |
| Characteristics |
infection: wild-type baculovirus SpltNPV
cell line: SL221
time point: 12hpi
|
| Treatment protocol |
SL221 cells infected with wild-type SpltNPV strain. Virus titers were determined by TCID50 (50 % tissue culture infective dose) end-point dilution assay using SL221 cells. SL221 cells were grown to the desired cell density and one million SL221 cells were inculated with SpltNPV (multiplicity of infection (MOI) = 1) in a T25 flask.
|
| Growth protocol |
SL221 cells were cultured in TNM-FH medium supplemented with 10% FBS at 28°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen RNeasy RNA mini kit.Total DNA was extracted with Qiagen AllPrep DNA Kit
Illumina Strand Specific RNA Sequencing. Illumina sequencing libraries were constructed following a modified strand-specific RNA seq protocol. In brief, 3 μg purified total RNA was used for isolation of coding RNA and non-coding RNA using ribo-zero kit for rRNA depletion, then isolated RNA were simultaneously eluted and fragmented in Elute-Prime-Fragment Mix at 94°C for 8 min. First-strand cDNA synthesis was carried out using SuperScriptII (Invitrogen, Carlsbad, CA) in the presence of hexamer random primer. Second-strand cDNA was synthesized at 16°C for 1 hour. After end-repair and dA-tailing, the DNA fragments were ligated with TruSeq adapter. The sample was amplified with TruSeq PCR primers and sequenced on the Illumina HiSeq2500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
The resulting cleaned reads of each sample was assembled as unigenes using the Trinity package with optimized k-mer length of 25, respectively. The assembled unigenes of all the samples were cleaned by removing redundancies and further assembled as all-unigenes using CD-HIT software. The cleaned reads of each sample were aligned to the assembled all-unigenes using FANSe2 allowing 7 nt mismatch, respectively[26]. The all-unigene with at least 10 mapped reads were considered as reliably assembled unigenes.
Unigene abundance measurements were generationed and normalized using EdgeR ; The normalized standard were counts per million (CPM)
Genome_build: None
Supplementary_files_format_and_content: tab-delimited text files include normalized CPM values and raw fragment counts for each Sample
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hanqi Yin |
| E-mail(s) |
yhqjndx@163.com
|
| Phone |
86-18926104647
|
| Organization name |
shanghai biochip corporation
|
| Street address |
libing road 151
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
86-21 |
| Country |
China |
| |
|
| Platform ID |
GPL20077 |
| Series (1) |
| GSE68037 |
Transcriptome Responses of the Host Spodoptera litura upon Spodoptera litura nucleopolyhedrovirus infection |
|
| Relations |
| BioSample |
SAMN03495893 |
| SRA |
SRX1001802 |
