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Series GSE85374 Query DataSets for GSE85374
Status Public on Aug 30, 2016
Title Direct interrogation of the role of H3K9 in metazoan heterochromatin function
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary We replaced the endogenous histones of Drosophila melanogaster with histones containing an H3K9R mutation to interrogate the role of H3K9 in heterochromatin formation and function. We queried heterochromatin formation through Formaldhyde Assisted Isolation of Regulatory Elements coupled with sequencing to examine nucleosome occupancy and Heterochromatin Protein 1a ChIP sequencing to determine the localization of the major reader of H3K9me. We found that regions of pericentromeric heterochromatin exhibit decreased HP1a and nucleosome occupancy in H3K9R mutants. To examine potential consequences of these changes of chromatin architecture, we performed total RNA-seq. In H3K9R mutants we observed increased levels of transposon and pIRNA cluster transcripts; however, the protein-coding transcriptome was similar to controls.
 
Overall design FAIRE-seq and total RNA-seq were performed in imaginal wing discs from 3rd instar Drosophila larvae. gDNA-seq samples are input samples for FAIRE-seq. HP1a ChIP-seq was performed from whole 3rd instar larvae. All three experiments were performed on endogenous histone mutants rescued with either a wild-type (HWT) or H3K9R mutant transgenic histone array. Experiments were carried out in duplicate or triplicate.
 
Citation(s) 27566777
Submission date Aug 09, 2016
Last update date May 15, 2019
Contact name Taylor Penke
E-mail(s) penke@email.unc.edu
Organization name University of North Carolina Chapel Hill
Department Genetics and Molecular Biology
Lab Robert Duronio
Street address 3344 Genome Sciences Building, 250 Bell Tower Drive
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platforms (2)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (22)
GSM2265945 K9R1_FAIRE-Seq
GSM2265946 K9R2_FAIRE-Seq
GSM2265947 K9R3_FAIRE-Seq
Relations
BioProject PRJNA338389
SRA SRP081201

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE85374_FAIRE_edgeR_peaks.txt.gz 1.3 Mb (ftp)(http) TXT
GSE85374_HP1a_edgeR_1kbwindows.txt.gz 2.9 Mb (ftp)(http) TXT
GSE85374_RNA_cufflinks.diff.gz 674.9 Kb (ftp)(http) DIFF
GSE85374_RNA_deseq2.txt.gz 463.7 Kb (ftp)(http) TXT
GSE85374_genomicDNA_coverage_fairepeaks.txt.gz 93.5 Kb (ftp)(http) TXT
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Processed data are available on Series record

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