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Sample GSM2292625 Query DataSets for GSM2292625
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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