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Series GSE119638 Query DataSets for GSE119638
Status Public on Jan 15, 2019
Title Detection of RNA–DNA binding sites in long noncoding RNAs
Organism Homo sapiens
Experiment type Other
Summary Triple helix is a potential mechanism how lncRNAs interact with the genome. Our in silico method (Triplex Domain Finder) is able to predict the binding sites of lncRNA MEG3 and GATA6-AS in the genome. In order to validate these predictions, we develop DBD-Capture-Seq to capture the DNA loci where the given RNA oligo binds to via triplex.
Method: Different RNA oligos are used The biotinylated RNA oligos (MEG3 TFR1, MEG3 TFR2, and GATA6-AS TFR1) were incubated with sheared genomic DNA to allow for triplex formation. After binding to streptavidin-coated beads, RNA-associated DNA was eluted and subjected to deep sequencing.
Control experiments were conducted in the absence of biotinylated RNA oligos.
 
Overall design We have used 3 RNA oligos (MEG3 TFR1, MEG3 TFR2 and GATA6-AS TFR1) for capturing their triplex-forming loci (all in duplicates). Input and control experiments were tested as well.
 
Contributor(s) Costa IG, Kuo C, Sentürk Cetin N
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Submission date Sep 07, 2018
Last update date Mar 22, 2019
Contact name Ivan G. Costa
E-mail ivan.costa@rwth-aachen.de
Organization name Institute for Computational Genomics
Department RWTH Aachen Medical Faculty
Street address Pauwelsstr. 19
City Aachen
State/province NRW
ZIP/Postal code 52074
Country Germany
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (8)
GSM3379769 no oligo rep1
GSM3379770 no oligo rep2
GSM3379771 MEG3 TFR1 rep1
Relations
BioProject PRJNA489807
SRA SRP160131

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
GSE119638_GATA6AS_TFR1-diffpeaks_p2.5_captured.bed.gz 1.7 Mb (ftp)(http) BED
GSE119638_GATA6AS_TFR1-diffpeaks_p2.5_control.bed.gz 613.5 Kb (ftp)(http) BED
GSE119638_MEG3_TFR1-diffpeaks_p2.5_captured.bed.gz 1.4 Mb (ftp)(http) BED
GSE119638_MEG3_TFR1-diffpeaks_p2.5_control.bed.gz 230.5 Kb (ftp)(http) BED
GSE119638_MEG3_TFR2-diffpeaks_p2.5_captured.bed.gz 1.2 Mb (ftp)(http) BED
GSE119638_MEG3_TFR2-diffpeaks_p2.5_control.bed.gz 200.8 Kb (ftp)(http) BED
GSE119638_RAW.tar 1.6 Gb (http)(custom) TAR (of BW)
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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