|
| Status |
Public on Feb 13, 2018 |
| Title |
Control 03 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal lysate
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Sex: female
age: 1 week old
genotype: btl>DHR78
tissue: Whole animal lysate
|
| Growth protocol |
One week old female DHR78 rescued mutants and controls (btl>DHR78) were raised on a 8% yeast, 9% sugar diet
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Eight biological replicates per genotype (n=12 females per sample) were collected. RNA was extracted using Trizol and pairs of biological replicates were pooled to obtain four biological replicates for further purification using an RNeasy Mini kit (Qiagen 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v3
Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly
Converted splice coordinates to genome coordinates with SamTranscriptomeParser
Generated ReadCoverage USeq file and ran DefinedRegionDifferentialSeq using Ensembl transcripts and default settings
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
Nov 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Carl Thummel |
| Organization name |
University of Utah
|
| Department |
Human Genetics
|
| Lab |
Carl Thummel
|
| Street address |
15 N 2030 E Rm 2100
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112-5330 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE106866 |
Adult functions for the Drosophila DHR78 nuclear receptor |
|
| Relations |
| Reanalyzed by |
GSM3284498 |
| BioSample |
SAMN08024402 |
| SRA |
SRX3389651 |
