|
| Status |
Public on Dec 04, 2018 |
| Title |
D. mauritiana_stage2_replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
single embryo
|
| Organism |
Drosophila mauritiana |
| Characteristics |
embryonic stage: stage 2
replicate number: replicate 3
raw data mixed with d. melanogaster?: no
|
| Treatment protocol |
Eggs were collected from vials, and imaged to determine stage
|
| Growth protocol |
All species were maintained on molasses food in uncrowded conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TRIzol reagent extraction of total RNA from single embryos.
Libraries were constructed using Illumina Tru-Seq kits and indices
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff5
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.
|
| |
|
| Submission date |
Apr 09, 2018 |
| Last update date |
Aug 29, 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 |
GPL21269 |
| Series (1) |
| GSE112858 |
Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo |
|
| Relations |
| Reanalyzed by |
GSM4054510 |
| BioSample |
SAMN08899782 |
