|
Status |
Public on Jan 04, 2017 |
Title |
D. pse female 3 (targeted seq) |
Sample type |
SRA |
|
|
Source name |
female whole body
|
Organism |
Drosophila pseudoobscura |
Characteristics |
developmental stage: 5 day old adult replicate: 1 library strategy: targeted sequencing strain: UCSD stock: 14011-0121.94
|
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 MiSeq |
|
|
Description |
6species_female_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 |
GPL22420 |
Series (2) |
GSE86055 |
Evolution of A-to-I RNA Editing in Drosophila |
GSE86056 |
A-to-I RNA Editing in Drosophila |
|
Relations |
BioSample |
SAMN05645870 |
SRA |
SRX2053374 |