 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 30, 2020 |
| Title |
Mitochondrial - Y Chromosome Epistasis in Drosophila melanogaster |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We generate 36 otherwise isogenic Drosophila melanogaster strains differing only in the geographical origin of their mitochondrial genome and Y chromosome to experimentally examine the effects of the uniparentaly inherited parts of the genome, as well as their interaction, in males. We assay gene expression through RNA-sequencing and detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis.
|
| |
|
| Overall design |
We used a 6x6 crossing design, crossing females from six mitochondrial replacement lines with males from six Y chromosome replacement lines, resulting in male offspring with 36 mito-Y combinations. Mitochondrial and Y Replacement lines share the same 4361 nuclear background, which means our 36 mitochondrial-Y replacement lines are isogenic outside of their mitochondrial haplogroup and Y haplotype. Mitochondrial genomes came from Beijing, China (2 lines; B38 and B39), Ithaca, NY, USA (1 line; I02), and the Netherlands (3 lines; N01, N02, and N23), and the Y chromosomes from Beijing, China (2 lines; B04 and B11), the Netherlands (2 lines; N03 and N07), and Zimbabwe (2 lines ; ZWH123 and YZW139). These populations represent deeply divergent mitochondrial and Y chromosome clades chosen from the Global Diversity Lines. We performed RNA sequencing on 10 3-5 day old males from each of the 36 mitochondrial-Y combinations. We used two biological replicates for each combination, with individuals for each replicate being collected from separate crosses between females from the mitochondrial-replacement and males from the Y-replacement parental lines performed on the same day.
|
| Web link |
https://pubmed-ncbi-nlm-nih-gov.proxy.library.cornell.edu/33081607/
|
| |
|
| Contributor(s) |
Ågren JA, Munasinghe MA, Clark AG |
| Citation(s) |
33081607 |
| |
| Submission date |
Jul 29, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Andrew Clark |
| Organization name |
Cornell University
|
| Street address |
215 Tower Road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
|
| Samples (72)
|
|
| Relations |
| BioProject |
PRJNA649569 |
| SRA |
SRP274159 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE155395_DESeq2_normalized_gene_counts.csv.gz |
7.0 Mb |
(ftp)(http) |
CSV |
| GSE155395_RAW.tar |
4.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE155395_raw_gene_counts.csv.gz |
1.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...