|
| Status |
Public on Nov 30, 2017 |
| Title |
WR Dv-1 cells control rep2 |
| Sample type |
SRA |
| |
|
| Source name |
WR Dv-1 cell
|
| Organism |
Drosophila virilis |
| Characteristics |
cell type: First instar larval derived cells
transfecting vector: pUAST-only
|
| Treatment protocol |
Cells were transfected in 48-well plates with 100 ng of ub-GAL4 and 200 ng of conspecific pUAST-mir-975 or empty vectors (pUAST only) using Lipofectamine 2000 (Thermo Fisher Scientific, catalog no.12566014), and were harvested 48 hours after transfection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from cells using TRIzol (Thermo Fisher Scientific, catalog no. 15596026)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Pipeline from Beijing Genomics of Institute (Shenzhen) was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the conspecific Drosophila whole genome using TopHat (v.1.3.1) with the parameter -r 20
Gene expression was estimated as FPKM (Fragments Per Kilobase Million) using Cufflink (v.2.1.1) with default parameters. Differentially expressed genes were estimated using Cuffdiff (v.2.1.1) with default parameters.
Genome_build: D. melanogaster BDGP5.19, D. simulans WUGSC1.19 and D. virilis caf1.19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Nov 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yang Lyu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Street address |
109 Zina Pitcher Place
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13313 |
| Series (1) |
| GSE107390 |
miR-975 overexpression effect on Drosophila cell lines |
|
| Relations |
| BioSample |
SAMN08102400 |
| SRA |
SRX3424882 |
