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Series GSE132191 Query DataSets for GSE132191
Status Public on Dec 05, 2019
Title RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (CAGE)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs,, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However they present still some limitations. Here, we introduce RNA and DNA interacting complexes ligated and sequenced (RADICL-seq), a novel technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation based methodology that reduces the bias for nascent transcription, increases genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.
 
Overall design Identification of genome-wide RNA-chromatin interactions in 2 cell types
 
Contributor(s) Bonetti A, Carninci P
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Submission date Jun 04, 2019
Last update date Dec 07, 2019
Contact name Kosuke Hashimoto
E-mail(s) kosuke.hashimoto@riken.jp
Organization name RIKEN
Department IMS
Street address 1-7-22 Suehiro-cho, Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 224-0001
Country Japan
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (6)
GSM3852792 mESC_CAGE_n1
GSM3852793 mESC_CAGE_n2
GSM3852794 mESC_CAGE_n3
This SubSeries is part of SuperSeries:
GSE132192 RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Relations
BioProject PRJNA546284
SRA SRP200422

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
GSE132191_RAW.tar 136.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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