Data from: Genome-wide errant targeting by Hairy

Kok K, Ay A, Li LM, Arnosti DN

Date Published: September 21, 2015

DOI: http://dx.doi.org/10.5061/dryad.cv323

 

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Title Microarray_raw_data.tar
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Description Expression profiling analysis: Transcriptome data from four biological replicates were generated using 8x15K Customized Drosophila Genome Oligo Microarrays (Agilent). Slide image data was quantified using Agilent's Feature Extraction software.
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Title diffReps_files.tar
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Description Differentially changed genomic regions for histone marks were identified using the diffReps program, which uses a sliding window approach to scan the genome and find regions showing read count differences. Regions detected by diffReps were associated with genes by identifying the nearest RefSeq TSS and annotated to a genomic feature such as intergenic, intron, exon etc.
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Title HOMER_peak_files.tar
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Description Using HOMER with default settings, peaks for histone marks and Flag tagged Hairy protein were identified using signals from H3 ChIP and input respectively as background. Peaks called by HOMER were associated with genes by identifying the nearest RefSeq TSS and annotated to a genomic feature such as intergenic, intron, exon etc.
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Title bedgraph_files.tar
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Description ChIP-Seq experiments were visualized as custom tracks using Integrative Genomics Viewer (Broad Institute). Total uniquely mapped tags were normalized to 10 million reads to generate tracks using HOMER.
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Title Machine_learning_CodeANDResults
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Description To perform machine learning analysis to predict genes in the repressed and not-repressed categories, we wrote Python and Java codes to partition our dataset into 10 parts to perform feature selection and 10-fold cross validation classification utilizing the Weka machine learning software. The folder includes the codes used in this analysis and raw results that are summarized in the main text. For further description, a readme file is provided under WekaCode folder.
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Title bed_files.tar.gz part a
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Description Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files.tar.gz folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
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Title bed_files.tar part b
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Description Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
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Title bed_files.tar part c
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Description Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
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Title bed_files.tar part d
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Description Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
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Title bed_files.tar part e
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Description Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
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When using this data, please cite the original publication:

Kok K, Ay A, Li LM, Arnosti DN (2015) Genome-wide errant targeting by Hairy. eLife 4: e06394. http://dx.doi.org/10.7554/eLife.06394

Additionally, please cite the Dryad data package:

Kok K, Ay A, Li LM, Arnosti DN (2015) Data from: Genome-wide errant targeting by Hairy. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cv323
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