|
| Status |
Public on Mar 01, 2020 |
| Title |
16046X16 |
| Sample type |
SRA |
| |
|
| Source name |
ERR mutant
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: ERR mutant
tissue: whole fly
time point: P2
|
| Treatment protocol |
All animals were subjected to heat-treatment on days 4 and 5 AEL. Experimental and control animals differed in their genotype (presence or absence of hsFLP transgene)
|
| Growth protocol |
Animals were staged as WPP for timecourse collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zymo Direct-zol RNA miniprep kit (with DNase treatment)
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10) with UDI. Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371) . Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Optical duplicates were removed with clumpify, adapter trimming was performed with cutadapt (version 1.16), and alignment was done using STAR (version 2.7.0f). Transcript expression was quantified with RSEM v1.3.1 (Li and Dewey 2011) following alignment to the dm6 genome (Ensembl release 96) with STAR v2.7.0f (Dobin et al. 2013).
Genome_build: dm6
Supplementary_files_format_and_content: excel file, has raw counts, normalized counts, vsd log counts (DESeq2 version 1.22.2), fpkm values, and sample IDs.
|
| |
|
| Submission date |
Feb 04, 2020 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Katherine Beebe |
| E-mail(s) |
kbeebe@genetics.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Molecular Medicine
|
| Lab |
Dr. Aylin Rodan
|
| Street address |
15 North 2030 East
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE144764 |
Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis [RNA-Seq timecourse] |
| GSE144766 |
Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis |
|
| Relations |
| BioSample |
SAMN13991828 |
| SRA |
SRX7673067 |
