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Sample GSM4295319 Query DataSets for GSM4295319
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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