|
| Status |
Public on Mar 06, 2023 |
| Title |
total-RNA_Siwi-KD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured cell derived from ovary
|
| Organism |
Bombyx mori |
| Characteristics |
cell line: BmN4
tissue: Cultured cell derived from ovary
genotype: Siwi KD
treatment: RNAi
|
| Treatment protocol |
BmN4 cells (0.5-1.5×10^6 cells) suspended in 100 μL of EP buffer [137 mM sodium chloride, 5 mM potassium chloride, 0.5 mM sodium hydrogen phosphate, and 2.1 mM HEPES-KOH (pH 7.1)] were transfected with 500-750 pmol siRNA duplex by electroporation with Nucleofector 2b (Lonza). Luciferase (Luc) siRNA was used as a control.
|
| Growth protocol |
BmN4 cells were cultured at 26°C in EX-CELL 420 serum-free medium for insect cells (Sigma-Aldrich) supplemented with 10% fetal bovine serum (Gibco) and 1× penicillin-streptomycin-glutamine (Thermo Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA sequencing: BmN4 cells treated with Luc (control) or Siwi siRNA were used for RNA sequencing. Total RNAs were isolated using ISOGEN II (FUJIFILM Wako Pure Chemical) and DNase (Life Technologies).
total RNA sequencing: RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with the Ribo-Zero Plus rRNA Depletion Kit (Human/Mouse/Rat) (Illumina) and sequenced on the NovaSeq platform (Illumina) to obtain paired-end reads, resulting in 77,614,516 and 68,702,400 reads for Luc KD and 81,135,072 and 77,184,922 reads for Siwi KD (Replicates 1 and 2, respectively).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
total RNA sequencing: After cleaning raw reads and removal of adaptor sequences using Rcorrector (version 1.0.4) (Song et al. 2015), TranscriptomeAssemblyTools (https://github.com/harvardinformatics/TranscriptomeAssemblyTools), and TrimGalore (version 0.6.6) (https://github.com/FelixKrueger/TrimGalore), reads shorter than 36 nt were discarded. The reads were mapped against the genome and remapped against the silkworm gene library using STAR in random and multiple counting modes allowing up to 4% mismatches relative to read length. Gene-mapped reads from the total RNA sequencing data were processed using SAMtools. The reads mapped to the sense direction were normalized against the number of genome-mapped reads to RPKM with the addition of a pseudo-count for log transformation and FC calculation. Owing to the high correlation of replicate samples, the two replicate reads were merged for further analysis.
Assembly: the Bombyx mori genome assembly (Nov 2016) (Kawamoto et al. 2019) from the SilkBase database
Supplementary files format and content: total RNA sequencing: Tab-separated text files include normalized count of reads (RPKM) mapped to the silkworm gene library in sense direction.
|
| |
|
| Submission date |
Sep 22, 2022 |
| Last update date |
Mar 07, 2023 |
| Contact name |
Yurika Namba |
| E-mail(s) |
yurika-namba@g.ecc.u-tokyo.ac.jp
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Biological Sciences, Graduate School of Science
|
| Lab |
Siomi Lab
|
| Street address |
2-11-16 Yayoi, Bunkyo-ku
|
| City |
Tokyo |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
| |
|
| Platform ID |
GPL29210 |
| Series (2) |
| GSE213915 |
Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association [RNA-Seq] |
| GSE213917 |
Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association |
|
| Relations |
| BioSample |
SAMN30959890 |
| SRA |
SRX17671497 |
