|
| Status |
Public on Jul 07, 2024 |
| Title |
Sample 6_S2 cells with dsRNA in the medium |
| Sample type |
SRA |
| |
|
| Source name |
Schneider2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Schneider2
cell type: hemocyte-like
genotype: wild-type
treatment: dsRNA in the medium
|
| Treatment protocol |
Samples 1-4: 70 nL of control saline or viral suspension (10e6 TCID50/mL) was injected into fly using Nanoject II. Flies were cultured for 24 hours and stored at -80°C until lysate preparation. Samples 5-10: dsRNA administration was carried out as described in Li & Zamore RNAi in Drosophila S2 Cells by dsRNA Soaking. Cold Spring Harb Protoc (2019). doi:10.1101/pdb.prot097477
|
| Growth protocol |
Samples 1-4 were maintained in a standard cornflour-yeast-glucose Drosophila food at 25°C. Sample 5-10 were maintained in Scheider's Drosophila medium supplimented with 10% FBS at 25°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lysates were prepared and immunoaffinity-purified with anti-Ago2 antibody as described in Kawamura et al. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453, 793–797 (2008). doi:0.1038/nature06938
Sequencing libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptor trimming and QC were done using Trim galore (v0.6.6)
21 nt reads were extracted using seqkit (v2.4.0)
Mapping of the trimmed reads on the reference genome was done using Bowtie (v1.3.1)
RNA counts were performed using featureCounts (v2.0.1)
Assembly: Ensembl Drosophila melanogaster BDGP6.32
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
|
| |
|
| Submission date |
Oct 03, 2023 |
| Last update date |
Jul 07, 2024 |
| Contact name |
Shingo Usuki |
| E-mail(s) |
usu@kumamoto-u.ac.jp
|
| Phone |
+81-96-373-5786
|
| Organization name |
Kumamoto University
|
| Department |
Institute of Molecular Embryology and Genetics (IMEG)
|
| Lab |
Liaison Laboratory Research Promotion Center
|
| Street address |
2-2-1 Honjo, Chuo-ku
|
| City |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE244523 |
Endocytosed dsRNAs induce lysosomal membrane permeabilization that allows cytosolic dsRNA translocation for Drosophila RNAi response |
|
| Relations |
| BioSample |
SAMN37657027 |
| SRA |
SRX21973712 |
