|
| Status |
Public on Nov 24, 2020 |
| Title |
D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 2, XY genotype |
| Sample type |
SRA |
| |
|
| Source name |
late stage 5 embryo
|
| Organism |
Drosophila mauritiana x Drosophila sechellia |
| Characteristics |
tissue: embryo
generation: F1 hybrid embryo
embryonic stage: late stage 5
embryo sex: XY genotype
replicate number: 2
|
| Treatment protocol |
Crosses between species as specified, to produce hybrid maternal transcriptomes for stage 2 embryos and hybrid zygotic transcriptomes for late stage 5 embryos.
|
| Growth protocol |
Cornmeal media, 25 degrees, population-controlled, eggs collected from mothers 4-14 days old.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent extraction of total RNA from single embryos.
Standard Illumina mRNA-Seq library prep protocols, using Illumina TruSeq kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mauxsec_st5_M_2
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt
|
| Data processing |
Adapter sequences trimmed using Cutadapt (v. 1.7.1).
Reads aligned to genomes using Tophat2 (v. 2.0.13).
Variants to identify allele-specific reads called using GATK haplotype caller.
Allele-specific reads counted using custom Python and R scripts (available with publication).
Counts normalized to upper quantile for total number of counts mapped per individual to a genome.
Genome_build: D. simulans (version r2.02); D. sechellia (version r1.3); D. mauritiana M17 assembly (Nolte et al., 2013; see Methods in publication).
Supplementary_files_format_and_content: *.txt: Allele-specific counts, mapping each hybrid individual to both parental genomes.
|
| |
|
| Submission date |
Aug 29, 2019 |
| Last update date |
Nov 24, 2020 |
| 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 |
GPL27402 |
| Series (1) |
| GSE136646 |
Evolved differences in cis and trans regulation between the maternal and zygotic mRNA complements in the Drosophila embryo |
|
| Relations |
| BioSample |
SAMN12659546 |
| SRA |
SRX6772327 |
