|
Status |
Public on Feb 14, 2014 |
Title |
pse_st2_6 |
Sample type |
SRA |
|
|
Source name |
embryo
|
Organism |
Drosophila pseudoobscura |
Characteristics |
tissue: embryo maternal genotype: Flagstaff 14 paternal genotype: PP1134 Sex: NA illumina index: 1
|
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 |
GSM3090249 |
BioSample |
SAMN02464304 |
SRA |
SRX396012 |