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Series GSE107131 Query DataSets for GSE107131
Status Public on Jan 01, 2020
Title U1 snRNP regulates chromatin retention of noncoding RNAs
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary RNA subcellular localization often correlates with its function and regulation. For many long noncoding RNAs (lncRNAs) and some isoforms of coding genes, their transcripts are preferentially retained on the chromatin. However, the mechanisms controlling the chromatin retention of lncRNAs and mRNA transcripts remain largely unknown. We hypothesize that embedded RNA sequences and interacting proteins may be the cis and trans regulators governing RNA subcellular localization, respectively. To comprehensively identify the cis-regulatory elements of RNA transcript, here we have developed a high-throughput sequencing-based method named RNA elements for subcellular localization by sequencing (REL-seq). Using this method, we identified RNA sequences contribute to the chromatin retention of several transcripts. By combining REL-seq with random mutagenesis (mutREL-seq), we further narrowed down the key RNA motifs and residues in regulating their subcellular localization at base resolution. Finally, based on the RNA element we identified, we revealed and confirmed U1 snRNA targeting site contributes to RNA chromatin retention.
 
Overall design All RNA-seq(s) were designed to reveal differentially subcellular localized RNAs of RSLP library targeted genes.
 
Contributor(s) Yin Y, Lu J, Shen X
Citation(s) 32238924
Submission date Nov 20, 2017
Last update date Apr 10, 2020
Contact name jinlong lu
E-mail(s) bioyuyang@hotmail.com
Phone 5853098469
Organization name University of Rochester
Lab Gorbunova & Seluanov Labs
Street address 213 Hutchinson Hall
City Rochester
State/province NY
ZIP/Postal code 14627
Country USA
 
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (12)
GSM2861589 3AI-RTM-293T
GSM2861590 3AI-Xist-293T
GSM2861591 3AI-Xist-46C
Relations
BioProject PRJNA419135
SRA SRP125289

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE107131_RAW.tar 10.0 Kb (http)(custom) TAR (of TXT)
GSE107131_RTM_samples_reads_density_comparison.txt.gz 127.4 Kb (ftp)(http) TXT
GSE107131_Xist_samples_reads_density_comparison.txt.gz 47.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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