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Series GSE95514 Query DataSets for GSE95514
Status Public on Jun 08, 2017
Title Structure-seq2: Sensitive and accurate genome-wide profiling of RNA structure in vivo
Organism Oryza sativa Japonica Group
Experiment type Expression profiling by high throughput sequencing
Other
Summary We present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity and data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. Structure-seq2 can employ a biotinylated nucleotide to facilitate the protocol. We have benchmarked Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa) and apply Structure-seq2 to provide evidence of hidden breaks in chloroplast rRNA and a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded rRNA.
 
Overall design 14 Structure-seq2 libraries are generated via MiSeq. Two replicates are included each of the standard Structure-seq2 protocol (both + and - DMS), and of the biotin variation.
 
Contributor(s) Ritchey LE, Su Z, Tang Y, Tack D, Assmann SM, Bevilacqua PC
Citation(s) 28637286
Submission date Feb 28, 2017
Last update date May 15, 2019
Contact name Zhao SU
Organization name The Penn State University
Department Biology
Lab Sarah Assmann
Street address 354 N. Frear
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platforms (1)
GPL22703 Illumina MiSeq (Oryza sativa Japonica Group)
Samples (27)
GSM2515732 Structure-seq2 (-DMS) Rep1 [Standard_primer_A]
GSM2515733 Structure-seq2 (-DMS) Rep2 [Standard_primer_B]
GSM2515734 Structure-seq2 (+DMS) Rep1 [Standard_primer_C]
Relations
BioProject PRJNA377316
SRA SRP100858

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95514_All_info.xls.gz 1.8 Mb (ftp)(http) XLS
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