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Series GSE70181 Query DataSets for GSE70181
Status Public on Aug 12, 2015
Title Comparison of Hi-C results using in-solution versus in-nucleus ligation
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing "in-nucleus ligation" and the standard "in-solution ligation". The results show that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. Thus in-nucleus ligation not only simplifies the experimental procedures, but also produces higher quality data with benefits for the entire range of 3C applications.
Overall design We created Hi-C libraries by two different methods, in-solution ligation and in-nucleus ligation, from two biological replicates each of mouse foetal liver cells (mouse-1 and mouse-2) and human ES cells (human-1 and human-2) or the mixture of these two species. We also sequenced a random ligation library prepared by reversal of the cross-links and purification of the DNA prior to ligation.
Contributor(s) Nagano T, Várnai C, Schoenfelder S, Javierre B, Wingett SW, Fraser P
Citation(s) 26306623
Submission date Jun 23, 2015
Last update date May 15, 2019
Contact name Steven William Wingett
Organization name MRC Laboratory of Molecular Biology
Department Cell Biology
Street address Francis Crick Avenue, Cambridge Biomedical Campus
City Cambridge
State/province Cambs
ZIP/Postal code CB2 0QH
Country United Kingdom
Platforms (7)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL15103 Illumina HiSeq 1000 (Mus musculus)
GPL15433 Illumina HiSeq 1000 (Homo sapiens)
Samples (13)
GSM1718020 Human sample1: Hi-C in-nucleus ligation
GSM1718021 Human sample1: Hi-C in-solution ligation
GSM1718022 Human sample2: Hi-C in-nucleus ligation
BioProject PRJNA287806
SRA SRP059793

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE70181_RAW.tar 4.3 Gb (http)(custom) TAR (of TXT)
GSE70181_hicup_report_ISL_INL_RL.txt.gz 3.0 Kb (ftp)(http) TXT
GSE70181_powerlaw_curves.txt.gz 4.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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