|
| Status |
Public on Jul 30, 2020 |
| Title |
4-4_mtN01-YN07-1 |
| Sample type |
SRA |
| |
|
| Source name |
10 pooled 3-5 day old whole fly males
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole fly
Sex: male
mitochondrial haplogroup: Global Diversity Line N01
y haplotype: Global Diversity Line N07
bio replicate: A
batch: 1
|
| Treatment protocol |
N/A - this experiment was only to look at differences between otherwise isogenic lines w/ unique mitochondrial-Y combinations
|
| Growth protocol |
All flies during the crossing process were maintained in vials on standard sucrose-yeast medium in climate controlled growth chambers with a 12:12 hours light:dark cycle at 25℃
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each sample, 10 3-5 day old adult males were collected, pooled, and flash frozen on dry ice. RNA was harvested using a Trizol reagent. Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used.
RNA libraries were prepared for sequencing using standard Illumina protocols accompannying the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All Scripts Used For Processing + Analysis Can Be Found on github.com/mam737/mitoY_RNASEQ
FastQC v0.11.5 - evaluate quality of raw reads
Trimmomatic v0.36 - remove low qualtiy reads, crop first 10 bp, remove adapters, and drop reads shorter than 20 bp long
Star v2.6- align reads to reference genome
HTSeq-Count v0.11.0 - count reads
DESeq2 - Differential Expression Analsis
Genome_build: Drosophila melanogaster Genome Reference 6.18
Genome_build: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.18_FB2017_05/
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Jul 30, 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 |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE155395 |
Mitochondrial - Y Chromosome Epistasis in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN15671271 |
| SRA |
SRX8845828 |
