|
| Status |
Public on Mar 25, 2015 |
| Title |
D.mel 2 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila melanogaster_head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 0-2 day old adult
replicate: 2
gender: female
tissue: head
|
| Growth protocol |
Heads were dissected from adult female flies ages 0-2 days old.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fly heads.
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
mmPCR-seq
|
| Data processing |
Library strategy: microfluidic multiplex PCR (mmPCR-seq)
Primer sequences were trimmed off paired or single-end sequencing reads before mapping to both the dm3 and droSec1 genomes plus 120bp of exonic sequence surrounding known splice junctions using BWA allowing 10 mismatches per read.
Custom python scripts were used to determine the species origin of each read based on matches to the genome outside of editing sites and the A and G counts at known editing sites.
RNA editing levels were calculated as the percentage of G reads at each site.
Genome_build: dm3/droSec1
Supplementary_files_format_and_content: Processed data files include editing levels of D. melanogaster alleles and D. sechellia alleles in each sample. The tab delimited columns are formatted, D. melanogaster chromosome, position, D. mel A reads, D. mel G reads, D. mel editing level, D. sec A reads, D. sec G reads, D. sec editing level.
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Billy Li |
| E-mail(s) |
jin.billy.li@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
300 Pasteur Dr, Alway M341
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE67236 |
Cis regulatory effects on A-to-I RNA editing in Drosophila melanogaster, Drosophila sechellia and their F1 hybrids |
|
| Relations |
| BioSample |
SAMN03445194 |
| SRA |
SRX967480 |
