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Sample GSM2856200 Query DataSets for GSM2856200
Status Public on Feb 13, 2018
Title Control 01
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 GSM3284496
BioSample SAMN08024396
SRA SRX3389649

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

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