|
| Status |
Public on Apr 17, 2019 |
| Title |
Bm_15 |
| Sample type |
SRA |
| |
|
| Source name |
Sf9 cells with Bm-15 overexpression
|
| Organism |
Spodoptera frugiperda |
| Characteristics |
cell type: Ovary cells
passage: 15-18
genotype/variation: Bm-15 overexpression
|
| Treatment protocol |
For transient expression, cells were grown in 24-well plates to 70%-80% confluency and further transfected with 2μg of plasmid DNA or antisense oligonucleotides employing Lipofectamine LTX and Plus Reagents (Thermo Fisher Scientific). Cells were harvested at different time-points after transfection and subjected to further analysis.
|
| Growth protocol |
Sf9 cells were maintained in Grace medium (Gibco) containing 10% fetal bovine serum (FBS) (Gibco) at 28°C and routinely passaged every third day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from different samples of Sf9 cells with the TRIzol (Thermo Fisher Scientific) method.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA or by removing rRNAs from the total RNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeq™ 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Transcriptome de novo assembly is carried out with short reads assembling program – Trinity
Unigenes were annotated with the databases of NR, NT, Swiss-Prot, KEGG, COG and GO
WEGO software was used to do GO functional classification for all Unigenes
Unigene pathway analysis is used by KEGG
SNP analysis was analyzed by SOAP, SSR detection is done with software MicroSAtellite(MISA)
Genome_build: from SPODOBASE, All ESTs sequences (254639) come from 10 different libraries
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dandan Li |
| E-mail(s) |
lidannytc@126.com
|
| Phone |
86-13781771513
|
| Organization name |
Nanyang Normal University
|
| Lab |
Henan Key Laboratory of Insect Biology in Funiu Mountain
|
| Street address |
1638 Wolong Road
|
| City |
Nanyang |
| State/province |
Henan |
| ZIP/Postal code |
86-473061 |
| Country |
China |
| |
|
| Platform ID |
GPL17152 |
| Series (1) |
| GSE98196 |
De novo sequencing of transcriptome of Sf9 cells after Bm-15 overexpression and repression |
|
| Relations |
| BioSample |
SAMN06830802 |
| SRA |
SRX2764650 |
