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Series GSE84287 Query DataSets for GSE84287
Status Public on Jun 04, 2020
Title A novel method for genome-wide profiling of poly(A)-tail lengths
Organism Homo sapiens
Experiment type Other
Summary Polyadenylation at the 3’ end of eukaryotic messenger RNAs enhances mRNA stability and translational efficiency. Global analysis for poly(A) tail lengths may shed lights on various aspects of gene regulation studies. Two NGS-based methods have been introduced for genome-wide poly(A) profiling, and they have shown human poly(A) profiles with shorter than previously conceived tail lengths. However, both methods are technically challenging and difficult to be repeated or widely adapted. Here we present a more straightforward method for poly(A) profiling. Poly(A)-seq performed on Illumina NextSeq 500 produces single-end 300 nt reads that covers the entirety of poly(A) tails, and poly(A) lengths can be directly calculated from base call data. With Poly(A)-seq we report that the global poly(A) lengths of several human cell lines may be longer than previously reported. We also show that the size selection step during Poly(A)-seq library preparation may greatly affect the sequencing profile, and thus cautions should be taken for comparisons between samples. As a convenient tool, we hope wide applications of Poly(A)-seq helps to bring better understanding of poly(A) tail properties and functions.
Overall design The poly(A) length profiles of human HeLa (wild-type and siPTB), HEK293T and HCT116 cells were examined.
Contributor(s) Wang W, Yu F, Zhou Z, Zhang Y, Cheng C, Rang W, Wu Q, Zhang Y
Citation(s) 32544193
Submission date Jul 12, 2016
Last update date Sep 03, 2020
Contact name Dong Chen
Organization name ABLife, Inc.
Department Center for Genome Analysis
Street address 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
City Wuhan
State/province Hubei
ZIP/Postal code 430075
Country China
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (10)
GSM2522818 HeLa_PolyA_seq_1
GSM2522819 HeLa_PolyA_seq_2
GSM2522820 si-PTB_PolyA_seq_1
BioProject PRJNA328590
SRA SRP078310

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Supplementary file Size Download File type/resource
GSE84287_length_statistic.txt.gz 818 b (ftp)(http) TXT
GSE84287_polyA_len_summary_table_media.txt.gz 201.8 Kb (ftp)(http) TXT
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