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Sample GSM1232267 Query DataSets for GSM1232267
Status Public on Feb 22, 2014
Title 4C_Ibtk_rep3
Sample type SRA
Source name Trophoblast Stem Cells
Organism Mus musculus
Characteristics cell type: F1 hybrid trophoblast stem cells derived from blastocyst
passage: 17
strain: Cast/EiJ x C57BL/6
Treatment protocol TS cells were removed from feeder cells and grown feeder-free for 2 passages prior to fixation.
Growth protocol TS cells were cultured as previously described (Calabrese et al., 2012, Quinn et al., 2006)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted as fixed chromatin from nuclear lysates and fragmented by restriction digest. See methods in Williams et al., 2013
4C libraries were constructed using a modified, locus-specific protocol for 4C-Seq. See methods in Williams et al., 2013
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Sequences processed by CASAVA v1.8
Raw sequences were filtered for 4C-primers to identify anchor and allele of origin
Raw sequences were mapped using Bowtie v0.12.7 (-n 2 -l 100 -m 1 --best --strata)
Mapped sequences were processed using custom Perl scripts and the fourSig analysis package to identify significant interacting regions of the genome
Interacting regions were analyzed using custom R scripts to identify interacting fragments between replicate libraries and alleles
Genome_build: mm9
Supplementary_files_format_and_content: All text files are tab delimited and contain genomic coordinates for interactions and read counts.
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
Platform ID GPL13112
Series (1)
GSE50907 fourSig: A Method for Determining Chromosomal Interactions in 4C-Seq Data
BioSample SAMN02356746
SRA SRX351939

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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