|
| Status |
Public on Sep 15, 2018 |
| Title |
starved_trained_4hr_4 |
| Sample type |
SRA |
| |
|
| Source name |
starved_trained_4hr
|
| Organism |
Drosophila melanogaster |
| Characteristics |
training: trained
hours post-training: 4
precondition: starved
sugar: sucrose
tissue: fly head
replicate: 4
|
| Treatment protocol |
training as indicated
|
| Growth protocol |
Flies were maintained at 25 °C, with a 12:12 light:dark period.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After indicated behavioral treatment, individuals heads were collected on a dry-ice block and RNA was isolated with the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega).
Non-stranded RNA-Seq libraries were constructed using TRUSEQ RNA SAMPLE PREP KIT v2 from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rpkm.txt
starved_trained_4hr_4
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to Drosophila genome dm6 with tophat v2.0.13 using -g 1 and gene models in gtf format from Ensembl 84
Reads were quantified on reduced transcripts from genes in Ensembl 84 using the countOverlap function in the Bioconductor package GenomicFeatures.
RPKM values were determined using Bioconductor package edgeR version edgeR_3.18.1 using the count of mapped reads on the reduced exonic intervals for each gene.
Genome_build: dm6
Supplementary_files_format_and_content: rpkm.txt text file of expression values per sample in RPKM format.
|
| |
|
| Submission date |
Apr 18, 2018 |
| Last update date |
Sep 15, 2018 |
| Contact name |
Chris W Seidel |
| E-mail(s) |
seidel@phageT4.org
|
| Phone |
816 926 9054
|
| Organization name |
Stowers Institute
|
| Department |
Genomics
|
| Lab |
Seidel
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE113346 |
Associative appetitive olfactory conditioning with Sucrose in Drosophila at 1 and 4 hours post training |
| GSE113347 |
Antimicrobial peptides modulate long-term memory |
|
| Relations |
| BioSample |
SAMN08950890 |
| SRA |
SRX3962891 |
