NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1294535 Query DataSets for GSM1294535
Status Public on Feb 14, 2014
Title pse_st2_5
Sample type SRA
 
Source name embryo
Organism Drosophila pseudoobscura
Characteristics tissue: embryo
maternal genotype: Flagstaff 14
paternal genotype: PP1134
Sex: NA
notes: possibly unfertilized
illumina index: 2
Growth protocol Embryos were collected from crosses of 3-7 day old females, dechorionated, imaged using a compound microscope with DIC, and collected into Trizol and ruptured at the desired stage
Extracted molecule total RNA
Extraction protocol Standard Trizol extraction method, with the exception of using a large amount of reagent (1 mL) relative to the expected amount of extracted total RNA (~150ug), for ease of use
Illumina TruSeq kits and protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description pse.data.all.autonorm.txt (total RPKM)
pse.allele.spec.txt (allele specific RPKM)
Data processing Illumina CASAVA_v1.8.0 software used for base calling
Mapping with Bowtie, Tophat to both D. miranda and D. pseudoobscura genomes
Transcript abundances determined with Cufflinks
total RPKM renormalized to total autosomal read number (autosomes shared in both species)
allele specific counts per gene constructed as described in paper
Genome_build: D. pseudoobscura, Flybase 2.25. D. miranda, NCBI DroMir 1.0
Supplementary_files_format_and_content: RPKM values, .txt files
 
Submission date Dec 18, 2013
Last update date May 15, 2019
Contact name Susan E. Lott
Organization name University of California, Davis
Department Evolution and Ecoloty
Street address 2320 Storer Hall
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL13310
Series (1)
GSE53483 Sex-specific embryonic gene expression in species with newly evolved sex chromosomes
Relations
Reanalyzed by GSM3090248
BioSample SAMN02464298
SRA SRX396011

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap