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Sample GSM1642750 Query DataSets for GSM1642750
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
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
BioSample SAMN03445194
SRA SRX967480

Supplementary file Size Download File type/resource
GSM1642750_dmel-f-head-2_editing.txt.gz 11.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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