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E-GEOD-38079 - Composition and organization of active centromere sequences in complex genomes

Status
Released on 23 July 2012, last updated on 11 March 2013
Organism
Canis lupus familiaris
Samples (1)
Protocols (4)
Description
We report the sequences bound to CENP-A in the dog genome (Canis familiaris) for high-throughput characterization of centromeric sequences. We compare these ChIPSeq reads (72 bp, single read) against a reference centromeric satellite DNA domain database for the dog genome, resulting in the annotation of sequence variation and estimated abundance of seven satellite families together with adjacent, non-satellite sequences. To study global patterns of sequence diversity and characterizing the subset of sequences correlated with centromere function, these sequences were evaluated relative to a comprehensive centromere sequence domain k-mer library. From this analysis, we identify functional sequence features from two satellite families (CarSat1 and CarSat2) that are defined by distinct arrays subtypes. Sequences bound to CENP-A in MDCK (dog) cell line
Experiment type
ChIP-seq 
Contacts
Karen Elizabeth Hayden <geo@ncbi.nlm.nih.gov>, Huntington F Willard, Karen E Hayden
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-38079.idf.txt
Sample and data relationshipE-GEOD-38079.sdrf.txt
Processed data (1)E-GEOD-38079.processed.1.zip
Links