|
| Status |
Public on Feb 14, 2014 |
| Title |
mir_st2_1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Drosophila miranda |
| Characteristics |
tissue: embryo
maternal genotype: MSH22
paternal genotype: SP138
Sex: NA
illumina index: 3
|
| 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 |
mir.data.all.autonorm.txt (total RPKM)
mir.allele.spec.txt (allele specific RPKM)
mir.neoY.allele.spec.txt (allele specific neo-Y)
|
| 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 |
GPL18087 |
| Series (1) |
| GSE53483 |
Sex-specific embryonic gene expression in species with newly evolved sex chromosomes |
|
| Relations |
| Reanalyzed by |
GSM3090238 |
| BioSample |
SAMN02464290 |
| SRA |
SRX396001 |
