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Series GSE67959 Query DataSets for GSE67959
Status Public on Nov 16, 2015
Title Multiplexed analysis of chromosome conformation at vastly improved sensitivity
Organism Mus musculus
Experiment type Other
Summary Current methods for analysing chromosome conformation in mammalian cells are either insensitive and low resolution or low throughput. Since the methods are expensive and relatively difficult to perform and analyse they are not widely used outside of specialised laboratories. Here we have re-designed the Capture-C method producing a new approach, called next generation (NG) Capture-C, which solves most of the current setbacks in analysing chromosome conformation. NG Capture-C produces unprecedented levels of sensitivity and reproducibility, which can be used to analyse any number of genetic loci and/or many samples in a single experiment. NG Capture is straightforward to perform, requiring only standard reagents and access to basic next generation sequencing platforms. The complete and detailed protocol presented here, with new publically available tools for library design and data analysis, will allow most laboratories to analyse chromatin conformation at levels of sensitivity and throughput that were previously impossible.
 
Overall design NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, in this case the promoters of genes were exclusively used. The capture step has been optimised to markedly increase the sensitivity of the method (by introducing a double capture step), providing unprecedented levels of sensitivity and reliability for high resolution analysis of the chromatin landscape.
 
Contributor(s) Davies JO, Hughes JR
Citation(s) 26595209
Submission date Apr 16, 2015
Last update date May 15, 2019
Contact name James Oliver Joshua Davies
Organization name Weatherall Institute of Molecular Medicine, Oxford University
Department Molecular Haematology Unit
Lab Davies
Street address Weatherall Institute of Molecular Medicine, John Radcliffe Hospital
City Oxford
State/province Oxon
ZIP/Postal code OX3 9DU
Country United Kingdom
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (14)
GSM1659659 Hba-a1&2 Single Capture
GSM1659660 Hba-a1&2 Double Sample1 (same as Hba-a1&2 Single Capture)
GSM1659661 Hba-a1&2 Double Sample2
Relations
BioProject PRJNA281379
SRA SRP057265

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE67959_ALAS2-1_30gH_Nor_PF_BF.gfc.txt.gz 561.4 Kb (ftp)(http) TXT
GSE67959_ALAS2-2_30gH_Nor_PF_BF.gfc.txt.gz 655.4 Kb (ftp)(http) TXT
GSE67959_Adrb2_30gH_Nor_PF_BF.gfc.txt.gz 1.1 Mb (ftp)(http) TXT
GSE67959_CD47_30gH_Nor_PF_BF.gfc.txt.gz 556.7 Kb (ftp)(http) TXT
GSE67959_Epb4.9-Dematin_30gH_Nor_PF_BF.gfc.txt.gz 673.8 Kb (ftp)(http) TXT
GSE67959_EpoR_30gH_Nor_PF_BF.gfc.txt.gz 841.3 Kb (ftp)(http) TXT
GSE67959_GATA1_30gH_Nor_PF_BF.gfc.txt.gz 473.5 Kb (ftp)(http) TXT
GSE67959_Hba-1_30gH_Nor_PF_BF.gfc.txt.gz 947.5 Kb (ftp)(http) TXT
GSE67959_Hba-2_30gH_Nor_PF_BF.gfc.txt.gz 888.1 Kb (ftp)(http) TXT
GSE67959_HbaCombined_30gH_Nor_PF_BF.gfc.txt.gz 1.5 Mb (ftp)(http) TXT
GSE67959_HbaCombined_Best_Nor_PF_BF.gfc.txt.gz 2.4 Mb (ftp)(http) TXT
GSE67959_HbaCombined_Celln_Nor_PF_BF.gfc.txt.gz 2.0 Mb (ftp)(http) TXT
GSE67959_HbaCombined_Single_capture_PF_BF.gfc.txt.gz 51.5 Kb (ftp)(http) TXT
GSE67959_Hbb-b1_30gH_Nor_PF_BF.gfc.txt.gz 793.5 Kb (ftp)(http) TXT
GSE67959_Hbb-b2_30gH_Nor_PF_BF.gfc.txt.gz 988.4 Kb (ftp)(http) TXT
GSE67959_HbbCombined_30gH_Nor_PF_BF.gfc.txt.gz 1.4 Mb (ftp)(http) TXT
GSE67959_HbbCombined_Best_Nor_PF_BF.gfc.txt.gz 1.5 Mb (ftp)(http) TXT
GSE67959_HbbCombined_Celln_Nor_PF_BF.gfc.txt.gz 1.8 Mb (ftp)(http) TXT
GSE67959_HbbCombined_Fixation_Nor_PF_BF.gfc.txt.gz 4.6 Mb (ftp)(http) TXT
GSE67959_Hipk2_30gH_Nor_PF_BF.gfc.txt.gz 681.0 Kb (ftp)(http) TXT
GSE67959_ISCA1_30gH_Nor_PF_BF.gfc.txt.gz 861.8 Kb (ftp)(http) TXT
GSE67959_KLF1_30gH_Nor_PF_BF.gfc.txt.gz 891.1 Kb (ftp)(http) TXT
GSE67959_KLF3a_30gH_Nor_PF_BF.gfc.txt.gz 631.0 Kb (ftp)(http) TXT
GSE67959_KLF3b_30gH_Nor_PF_BF.gfc.txt.gz 854.6 Kb (ftp)(http) TXT
GSE67959_Klf4_30gH_Nor_PF_BF.gfc.txt.gz 507.6 Kb (ftp)(http) TXT
GSE67959_Lmo2-1_30gH_Nor_PF_BF.gfc.txt.gz 1.0 Mb (ftp)(http) TXT
GSE67959_Lmo2-2_30gH_Nor_PF_BF.gfc.txt.gz 639.5 Kb (ftp)(http) TXT
GSE67959_Mir144145_30gH_Nor_PF_BF.gfc.txt.gz 914.8 Kb (ftp)(http) TXT
GSE67959_NFE2_30gH_Nor_PF_BF.gfc.txt.gz 656.2 Kb (ftp)(http) TXT
GSE67959_Oct-4_30gH_Nor_PF_BF.gfc.txt.gz 753.4 Kb (ftp)(http) TXT
GSE67959_Pdzk1ip1_30gH_Nor_PF_BF.gfc.txt.gz 1.0 Mb (ftp)(http) TXT
GSE67959_Pkdrej_30gH_Nor_PF_BF.gfc.txt.gz 751.4 Kb (ftp)(http) TXT
GSE67959_Pnpo_30gH_Nor_PF_BF.gfc.txt.gz 987.3 Kb (ftp)(http) TXT
GSE67959_SOX2_30gH_Nor_PF_BF.gfc.txt.gz 521.4 Kb (ftp)(http) TXT
GSE67959_Slc25A37_30gH_Nor_PF_BF.gfc.txt.gz 851.7 Kb (ftp)(http) TXT
GSE67959_Slc25A37_Best_Nor_PF_BF.gfc.txt.gz 880.7 Kb (ftp)(http) TXT
GSE67959_Slc25A37_Celln_Nor_PF_BF.gfc.txt.gz 1.0 Mb (ftp)(http) TXT
GSE67959_Slc25A37_Fixation_Nor_PF_BF.gfc.txt.gz 2.4 Mb (ftp)(http) TXT
GSE67959_Sp2_30gH_Nor_PF_BF.gfc.txt.gz 973.4 Kb (ftp)(http) TXT
GSE67959_TP53_30gH_Nor_PF_BF.gfc.txt.gz 792.3 Kb (ftp)(http) TXT
GSE67959_Tal1-1_30gH_Nor_PF_BF.gfc.txt.gz 793.4 Kb (ftp)(http) TXT
GSE67959_Tal1-2_30gH_Nor_PF_BF.gfc.txt.gz 499.6 Kb (ftp)(http) TXT
GSE67959_Zcchc6_30gH_Nor_PF_BF.gfc.txt.gz 714.2 Kb (ftp)(http) TXT
GSE67959_cMyc-1_30gH_Nor_PF_BF.gfc.txt.gz 775.5 Kb (ftp)(http) TXT
GSE67959_cMyc-2_30gH_Nor_PF_BF.gfc.txt.gz 753.7 Kb (ftp)(http) TXT
GSE67959_nanog_30gH_Nor_PF_BF.gfc.txt.gz 999.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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