|
| Status |
Public on Dec 29, 2020 |
| Title |
SR_6h_1_2 |
| Sample type |
SRA |
| |
|
| Source name |
Seminal receptacle
|
| Organism |
Drosophila melanogaster |
| Characteristics |
time relative to matng: 6hr Postmating
strain: LHM
age: 3-8 days old
sequencing run: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Females were etherized (unmated, 6hrs, or 24hrs post-mating) and the female reproductive tract (FRT) removed in a drop of 1x PBS. The FRT was then microdissected into 6 discrete tissues. Tissues were rinsed in PBS and transferred directly to Trizol. Pooled tissue collections were homogenized with a pellet pestle and RNA was isolated using a phenol-chloroform extraction with phase-lock gels (ThermoFisher) and an overnight precipitation in isoproponal and 3M sodium acetate with 1.5ul glycogen (LifeTechnologies) at -18 C to maximize RNA recovery. The precipitation was followed by DNAse I (LifeTechnologies) treatment for 30 min at 37 C and a second RNA isolation. RNA was re-suspended in RNase-free H2O
RNA libraries were prepared for sequencing using standard protocols by Beijing Genomics Institute (BGI)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
sequenced reads were cleaned to remove adapter sequences and exclude reads with > 10% unknown bases of > 50% low-quality bases
sequenced reads were aligned to the D. melanogaster reference genome (r6.21) using hisat 2.1.0 with default settings plus the sam option to suppress reads that do not align or represent novel splice sites
read counts per million (CPM) were generated using StringTie
Genome_build: D. melanogaster reference genome (r6.21)
Supplementary_files_format_and_content: tab deliminated text file includes CPM value for each sample
|
| |
|
| Submission date |
Jan 15, 2020 |
| Last update date |
Dec 29, 2020 |
| Contact name |
Caitlin E McDonough |
| E-mail(s) |
mcdonouce@gmail.com
|
| Phone |
9176207629
|
| Organization name |
Syracuse University
|
| Department |
Syracuse University Biology Department
|
| Street address |
107 College Place, 114 Life Science Complex
|
| City |
Syracuse NY |
| State/province |
NY |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL26560 |
| Series (1) |
| GSE143759 |
Spatiotemporal female reproductive tract gene expression in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN13870075 |
| SRA |
SRX7569543 |
