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Series GSE50907 Query DataSets for GSE50907
Status Public on Feb 22, 2014
Title fourSig: A Method for Determining Chromosomal Interactions in 4C-Seq Data
Organism Mus musculus
Experiment type Other
Summary The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-seq experiments generate large, complicated datasets and it is imperative that signal is properly distinguished from noise. Currently there are a limited number of methods for analyzing 4C-seq data. Here, we present a new method, fourSig, which, in addition to being simple to use and as precise as current methods, also includes a new feature to prioritize significantly enriched interactions and predict their reproducibility among experimental replicates. Here, we demonstrate the efficacy of fourSig with previously published and novel 4C-seq datasets and show that our significance prioritization correlates with the ability to reproducibly detect interactions amongst replicates. The datasets provided include those generated from allele-specific 4C-Seq with a viewpoint of the TSS for the gene Ibtk on mouse Chromosome 9. FASTQ files, text files containing genomic coordiantes and read counts, and bedGraph formats for UCSC Genome Browser tracks are provided. All sequences were mapped relative to mouse genome build mm9.
Overall design Sequencing of circular chromosome conformation capture (4C-Seq) was performed at the transcription start site (TSS) for the gene Ibtk for three replicates in F1 hybrid mouse trophoblast stem (TS) cells. Experiment was designed to detect allele specific patterns using SNP differences between the inbred lines mated to produce the TS cells (C57Bl/6 and CAST/EiJ)
Contributor(s) Williams RL, Starmer J, Mugford JW, Calabrese JM, Mieczkowski P, Yee D, Magnuson T
Citation(s) 24561615
Submission date Sep 16, 2013
Last update date May 15, 2019
Contact name Rex Lee Williams
Organization name University of North Carolina
Department Genetics
Lab Magnuson Lab
Street address 120 Mason Farm Road
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (3)
GSM1232265 4C_Ibtk_rep1
GSM1232266 4C_Ibtk_rep2
GSM1232267 4C_Ibtk_rep3
BioProject PRJNA219332
SRA SRP029950

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Supplementary file Size Download File type/resource
GSE50907_Ibtk_B6cis_ReplicatedFragments.txt.gz 6.6 Kb (ftp)(http) TXT
GSE50907_Ibtk_CASTcis_ReplicatedFragments.txt.gz 6.3 Kb (ftp)(http) TXT
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Processed data are available on Series record

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