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Series GSE84170 Query DataSets for GSE84170
Status Public on Aug 14, 2016
Title 3’READS+, a sensitive and accurate method for 3’ end sequencing of polyadenylated RNA
Organism Homo sapiens
Experiment type Other
Expression profiling by high throughput sequencing
Summary Sequencing of the 3’ end of poly(A)+ RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3’ region extraction and deep sequencing (3’READS), to address mispriming issues that often plague 3’ end sequencing. Here we report a new version, named 3’READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)+ RNA and to remove bulk of the poly(A) tail, 3’READS+ generates RNA fragments with an optimal number of terminal As that balance data quality and detection of genuine pAs. With improved RNA ligation steps for efficiency, the method shows much higher sensitivity (over two orders of magnitude) compared to the previous version. Using 3’READS+, we have uncovered a sizable fraction of previously overlooked pAs located next to or within a stretch of adenylate residues in human genes, and more accurately assessed the frequency of alternative cleavage and polyadenylation (APA) in HeLa cells (~50%). 3’READS+ will be a useful tool to accurately study APA and to analyze gene expression by 3’ end counting, especially when the amount of input total RNA is limited.
 
Overall design Nine 3'READS+ libraries were made with different amounts (100 ng, 200 ng, 400 ng, 1000 ng, 5000 ng, 15000 ng) of input Hela RNA.
 
Contributor(s) Zheng D, Tian B
Citation(s) 27512124
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM084089 Regulation of Alternative Cleavage and Polyadenylation: Analysis of mRNA Polyadenylation across Species and Tissues RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY--RBHS-NEW JERSEY MEDICAL SCHOOL Tian
Submission date Jul 08, 2016
Last update date May 15, 2019
Contact name Bin Tian
E-mail(s) btian@wistar.org, dinghaiz@gmail.com
Organization name Rutgers University, New Jersey Medical School
Department Microbiology, Biochemistry and Molecular Genetics
Lab Bin Tian
Street address 205 South Orange Ave., F-Bay 7
City Newark
State/province NJ
ZIP/Postal code 07103
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (9)
GSM2228463 3'READS+_100 ng input, batch 2
GSM2228464 3'READS+_200 ng input, batch 1
GSM2228465 3'READS+_200 ng input, batch 2
Relations
BioProject PRJNA328218
SRA SRP078132

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
GSE84170_clustered_unique_reads.csv.gz 2.9 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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