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Series GSE39096 Query DataSets for GSE39096
Status Public on Nov 06, 2012
Title Spark: A navigational paradigm for genomic data exploration
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Biologists possess the detailed knowledge critical for extracting biological insight from genome-wide data resources and yet they are increasingly faced with non-trivial computational analysis challenges posed by genome-scale methodologies. To lower this computational barrier, particularly in the early data exploration phases, we have developed an interactive pattern discovery and visualization prototype, Spark, designed with epigenomic data in mind. Here we demonstrate Spark’s ability to reveal both known and novel epigenetic signatures using genome-wide histone modification, DNA methylation, and transcription factor data from human embryonic stem cells.
Overall design Human embryonic stem cells (hESCs) were obtained from Cellular Dynamics as part of a large batch of cells prepared for the ENCODE Consortium and the RoadMap Epigenome Consortium. Cell growth and crosslinking conditions can be found at ChIP-seq experiments for the histone modifications have been described previously (Harris et al. 2010). The YY1ChIP assay was performed using 5x107 cells following the protocol provided at except that StaphA cells were blocked only with BSA before use and the pre-clearing step was omitted. ChIP and Input samples (10% of the amount of chromatin used per ChIP) were purified using the QIAquick PCR purification kit (QIAGEN) according to manufacturer’s instructions and purified eluates were dissolved in 50uls of water. ChIP libraries were created and sequenced as described previously (Harris et al. 2010) by the DNA Technologies Core Facility at the University of California-Davis ( Illumina read sequences were aligned to the reference human genome (hg18) using BWA (Li and Durbin 2009). FindPeaks 4.0.15 (Fejes et al. 2008) was subsequently used to detect enrichment peaks at an FDR of 0.01.
Contributor(s) O'Geen H, Nielsen CB, Farnham PJ
Citation(s) 22960372
Submission date Jul 03, 2012
Last update date May 15, 2019
Contact name Henriette O'Geen
Organization name UC Davis
Street address 1 Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (1)
GSM956127 USC_ChIPSeq_H1-hESC_YY1_UCDavis
BioProject PRJNA170002
SRA SRP014011

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Supplementary file Size Download File type/resource
GSE39096_FarnhamLabChIP_Protocol.pdf.gz 344.6 Kb (ftp)(http) PDF
GSE39096_RAW.tar 992.3 Mb (http)(custom) TAR (of BW, TXT, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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