|
| Status |
Public on Jun 01, 2017 |
| Title |
WT-3 (2) |
| Sample type |
SRA |
| |
|
| Source name |
Whole fly lysate
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genetic background: Canton S
age: 10-11 day old adults
genotype: wild-type
grandparental obesity: None
parental heterozygosity: None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flies were flash frozen in liquid nitrogen and RNA isolated using Trizol reagent. RNA was then further purified using the Qiagen RNeasy clean-up procedure.
Libraries were prepared using Illumina TruSeq Standard mRNA Library Preparation Kit polyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
12403X3_160520_D00294_0242_AC9B97ANXX_6
|
| Data processing |
base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v4
RNA-seq reads were aligned to the dm3 genome build with Ensembl transcript splice alignments using novoalign
Converted splice coordinates to genome coordinates with SamTranscriptomeParser
Generated ReadCoverage USeq file
Ran DefinedRegionDifferentialSeq using Ensembl transcripts and default settings
Data was corrected for batch effects between experimental replicates
Genome_build: dm3
Supplementary_files_format_and_content: xlsx file containing analyzed output from DESeq including counts of reads overlapping gene of interest, Variance corrected per gene in log space from DESeq, and FPKM
|
| |
|
| Submission date |
Apr 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Carl Thummel |
| E-mail(s) |
cthummel@genetics.utah.edu
|
| Organization name |
University of Utah School of Medicine
|
| Department |
Human Genetics
|
| Street address |
15 N 2030 E Rm 5200
|
| City |
SALT LAKE CITY |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE97525 |
F2 progeny of AKHR mutant and obese parents and controls, 10-11 days old adults |
|
| Relations |
| Reanalyzed by |
GSM3283299 |
| BioSample |
SAMN06700744 |
| SRA |
SRX2731292 |
