|
| Status |
Public on Sep 17, 2018 |
| Title |
MB-Naïve_3 |
| Sample type |
SRA |
| |
|
| Source name |
MB-Naïve, Mushroom body nuclei
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Mushroom body
age: adult males four to six days old
genotype: X; unc84-GFP/+;R14H06Gal4/attP2
treatment: Naïve
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. A whole head fraction (WH) was then taken from this homogenate as a representation of the whole fly head, containing both MB-specific GFP nuclei untagged non-MB nuclei. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from both WH and MB-fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Nugen Ovation Drosophila RNA-Seq System 1-16 (Nugen: NU035032) according to manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mushroom body nuclei extracted from socially isolated males, collected at the same time of day as 1h-AR and 24h-AR samples.
|
| Data processing |
Raw sequence reads were trimmed using Prinseq (version 0.20.4) quality trimming to a minimum base quality score of 30
Trimmed reads were aligned to D. melangaster genome (dm6, Ensembl release 88) using STAR. Reads were also aligned to C. elegans unc-84 gene (NC_003284.9). Only uniquely aligned reads with a maximum of four mismatches were used downstream.
Gene counts were obtained using HTSeq-count (version 0.7.1) using union setting to generate genic regions.
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for genic regions obtained using HTSeq
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Sep 17, 2018 |
| Contact name |
Spencer Gordon Jones |
| Organization name |
Dalhousie University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Kramer Lab
|
| Street address |
5850 College St
|
| City |
Halifax |
| State/province |
NS |
| ZIP/Postal code |
B3H4R2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE115718 |
Transcriptional profiling in Kenyon cells reveals dynamic regulation of learning and memory genes after acquisition of long-term courtship memory |
|
| Relations |
| BioSample |
SAMN09404293 |
| SRA |
SRX4201583 |
