|
| Status |
Public on Jan 04, 2017 |
| Title |
D. ana male 2 |
| Sample type |
SRA |
| |
|
| Source name |
male whole body
|
| Organism |
Drosophila ananassae |
| Characteristics |
developmental stage: 5 day old adult
replicate: 2
library strategy: mmPCR-seq
strain: UCSD stock: 14024-0371.13
|
| Growth protocol |
Whole bodies of adult male and female flies aged 5 days old were collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Rneasy Kit (Qiagen). After DNase I treatment, 3 ug of total RNA was used to synthesize the cDNA using iScript Advanced cDNA Synthesis Kit (Bio-Rad). cDNA was purified using the MinElute PCR Purification Kit (Qiagen)
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
microfluidic multiplex PCR (mmPCR-seq) or targeted sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
6species_male_wb_editing_levels.txt
|
| Data processing |
Primer sequences were trimmed off paired or single-end sequencing reads before mapping using Tophat.
RNA editing levels were calculated as the fraction of G reads at each site. Only sites covered by 50 reads were used
Genome_build: dm3/droSim1/droYak2/droAna2/dp3/droVir3
Supplementary_files_format_and_content: Processed data files are tab-delineated with a header line and include editing levels of different Drosophila strains and species.
|
| |
|
| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Billy Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
300 Pasteur Drive. Alway M303
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13309 |
| Series (2) |
| GSE86055 |
Evolution of A-to-I RNA Editing in Drosophila |
| GSE86056 |
A-to-I RNA Editing in Drosophila |
|
| Relations |
| BioSample |
SAMN05645883 |
| SRA |
SRX2053361 |
