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| Status |
Public on Nov 28, 2015 |
| Title |
Control bio replicate 1 |
| Sample type |
SRA |
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| Source name |
control_adult males
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: control
strain info.: EP/KG precise excision transheterozygote
gender/age: adult male
tissue: whole-animal
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| Growth protocol |
Flies were cultured under density-controlled conditions (~60 larvae per vial) raised on 3% sugar diet, then 5 day old adults were transferred to 15% sugar diet for 3 days prior to sample collection.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from dHNF4 mutants and genetically-matched control adult males (8 days old) using TriPure isolation reagent (Roche) followed by further purification/cleanup by RNeasy kit (QIAGEN)
RNA from 4 biological replicates (n=40 flies per sample) per genotype was polyA-selected and assembled into barcoded libraries and pooled into a single-flow cell lane for Illumina HighSeq2000 50-cycle single-read sequencing,
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly.
nohup java -jar -Xmx20G ~/AppsUSeq/OverdispersedRegionScanSeqs -s ODRSS/ -t BamAlignments/HNF4Mut/ -c BamAlignments/Control/ -u dm3EnsGenes.ucsc.gz -o -p -v D_melanogaster_Apr_2006 &> ODRSS/odrss.log.txt &
for x in $(ls *bam); do echo $x; java -jar -Xmx10G ~/AppsUSeq/SamParser -v D_melanogaster_Apr_2006 -f $x -r PD_$x -m 0 -a 120; done
nohup java -jar -Xmx10G ~/AppsUSeq/MultipleReplicaScanSeqs -s MRSS/ -t BamAlignments/HNF4Mut/ -c BamAlignments/Control/ -p 0 -w 200 -f 1 -b &> MRSS/mrss.log.txt &
jj ~/AppsUSeq/EnrichedRegionMaker -f MRSS/binaryWindowData.swi.zip -i 0,1 -s 10,1 -r dm3EnsGenes_Exons.bed.gz -b 1000jj ~/AppsUSeq/EnrichedRegionMaker -f MRSS/binaryWindowData.swi.zip -i 0,1 -s 10,1 -r dm3EnsGenes_Exons.bed.gz -b 1000 -m
Genome_build: dm3
Supplementary_files_format_and_content: Matrix excel file for differential mRNA adundance in treatment (T, aka dHNF4 mutants) versus control (C) samples including gene ID number, gene name, FDR, and log2 values
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| Submission date |
Sep 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Carl S Thummel |
| Organization name |
University of Utah, School of Medicine
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| Department |
Human Genetics
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| Lab |
Carl Thummel Lab
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| Street address |
15 N 2030 E, Room 5200
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (2) |
| GSE73523 |
Drosophila HNF4 promotes glucose-stimulated insulin secretion and increased mitochondrial function in adults [RNA-seq] |
| GSE73676 |
Drosophila HNF4 promotes glucose-stimulated insulin secretion and increased mitochondrial function in adults |
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| Relations |
| Reanalyzed by |
GSM3276805 |
| SRA |
SRX1293258 |
| BioSample |
SAMN04121959 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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