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Series GSE54414 Query DataSets for GSE54414
Status Public on Apr 13, 2014
Title Multiscale representation of genomic signals
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genomic information is encoded on a wide range of distance scales, ranging from tens of base pairs to megabases. We developed a multiscale framework to analyze and visualize the information content of genomic signals. Different types of signals, such as GC content or DNA methylation, are characterized by distinct patterns of signal enrichment or depletion across scales spanning several orders of magnitude. These patterns are associated with a variety of genomic annotations, including genes, nuclear lamina associated domains, and repeat elements. By integrating the information across all scales, as compared to using any single scale, we demonstrate improved prediction of gene expression from Polymerase II ChIP-seq measurements and we observed that gene expression differences in colorectal cancer are not most strongly related to gene body methylation, but rather to methylation patterns that extend beyond the single-gene scale.
 
Overall design ChIP-seq data of six proteins in primary murine bone marrow macrophage cells (BMMs) under unstimulated and lipopolysaccharide (LPS) stimulated conditions. The BMMs were cultured from female C57BL/6 mice (age 8-12 weeks). Amongst these six proteins were three transcription factors (TFs), ATF340, NFκB/p50 and NFκB/p65, all of which are involved in regulating macrophage activation by microbial molecular components such as LPS. The other three ChIP-seq targets were RNA polymerase II (Pol II), and two chromatin modification marks: acetylation of histone H4 (H4ac) and tri-methylation of histone H3 lysine 27 (H3K27me3).
 
Contributor(s) Knijnenburg TA, Ramsey SA, Kennedy KA, Aderem A, Shmulevich I
Citation(s) 24727652
Submission date Jan 27, 2014
Last update date Mar 08, 2019
Contact name Theo Knijnenburg
E-mail tknijnen@systemsbiology.org
Organization name Institute for Systems Biology
Street address 401 Terry Avenue North
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (35)
GSM1314649 20080606_1348_B_BMM_LPS_0060_P50
GSM1314650 20080723_1272_A_BMM_NoStim_0000_P50
GSM1314651 20080723_1273_A_BMM_LPS_0060_P50
Relations
BioProject PRJNA236459
SRA SRP035865

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Supplementary file Size Download File type/resource
GSE54414_RAW.tar 3.1 Mb (http)(custom) TAR (of BED)
Raw data are available in SRA
Processed data provided as supplementary file

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