Data from: The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults

Thummel CS, Barry WE

Date Published: June 3, 2016

DOI: http://dx.doi.org/10.5061/dryad.8h8q5

 

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Title dHNF4_RNAseq_DiffExpr_1.5fold
Downloaded 4 times
Description 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, which produced ≥ 21.9 million reads per sample. Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly. Transcripts meeting a cutoff of ≥1.5 fold difference in mRNA abundance (~Log2 ≥ +/- 0.6) and FDR ≤ 1% were considered as differentially expressed genes. RNA quality control, library preparation, sequencing, and data analysis were performed at the University of Utah High Throughput Genomics and Bioinformatics Core Facilities.
Download dHNF4_RNAseq_DiffExpr_1.5fold.xlsx (198.4 Kb)
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Title dHNF4_ChIPseq_NearestNeighbor
Downloaded 2 times
Description dHNF4-DNA bound complexes were immunoprecipitated using polyclonal antibody against endogenous dHNF4 protein. Barcoded libraries for dHNF4-IP and input control samples were generated by the University of Utah High Throughput Genomics core facility and sequenced in a single lane Illumina HiSeq 5-cycle single-read sequencing. Data analysis was performed by the Bioinformatics Core at the University of Utah School of Medicine using USeq and Model-based Analysis for ChIP-seq (MACS2) run with a peak shift of 100 bp. Enrichment peaks were identified with an FDR cutoff of 1% and nearest neighboring genes were compiled using USeq FindNeighboringGenes and UCSC dm3 EnsGenes gene tables. Nearest neighbor genes were compared to our RNA-seq dataset to identify neighbors that are also misexpressed in dHNF4 mutants, highlighting these as direct targets of dHNF4.
Download dHNF4_ChIPseq_NearestNeighbor.xlsx (74.67 Kb)
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When using this data, please cite the original publication:

Barry WE, Thummel CS (2016) The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults. eLife 5: e11183. http://dx.doi.org/10.7554/elife.11183

Additionally, please cite the Dryad data package:

Thummel CS, Barry WE (2016) Data from: The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8h8q5
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