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Series GSE84068 Query DataSets for GSE84068
Status Public on Nov 20, 2017
Title Post-transcriptional 3’UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Here, using genome wide analysis, we demonstrate that canonical mRNA is processed post-transcriptionally through an alternative cleavage and polyadenylation mechanism. As a result of this process, the downstream cleavage fragment of the 3′UTR remains uncapped and stable
This finding indicates that different parts of gene mRNA are separate and independent, by re-annotating the human transcriptome using this model, we provide a new overview of the function and impact of microRNA (miRNA)
Our results shed new light on the mammalian transcriptome and show that what were considered as 3′UTRs are in fact autonomous RNA fragments.
Overall design Examination of mRNA levels and cleavage across transcripts in U2OS and 293 cell types (3 replicates each)
Contributor(s) Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, Margalit H, Kaplan T, Berger M
Citation(s) 29229900
Submission date Jul 06, 2016
Last update date May 15, 2019
Contact name Tommy Kaplan
Organization name Hebrew University
Department School of Computer Science and Engineering
Street address Givat Ram Campus
City Jerusalem
ZIP/Postal code 91904
Country Israel
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (36)
GSM2226713 mRNA U2OS cell rep 1
GSM2226714 mRNA U2OS cell rep 2
GSM2226715 mRNA U2OS cell rep 3
BioProject PRJNA327927
SRA SRP077969

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE84068_RAW.tar 3.8 Gb (http)(custom) TAR (of BIGWIG)
GSE84068_Supp_Table1_U2OS_TEX_fit_hmm.tsv.gz 3.4 Mb (ftp)(http) TSV
GSE84068_Supp_Table2_U2OS_5prime_fit_hmm.tsv.gz 3.2 Mb (ftp)(http) TSV
GSE84068_Supp_Table3_U2OS_3prime_fit_hmm.tsv.gz 3.3 Mb (ftp)(http) TSV
GSE84068_Supp_Table4_293_TEX_fit_hmm.tsv.gz 3.5 Mb (ftp)(http) TSV
GSE84068_Supp_Table5_3end_RNA-seq_peaks_prox+dist.tsv.gz 126.0 Kb (ftp)(http) TSV
GSE84068_Supp_Table6_293_Mir92_fit_hmm.tsv.gz 3.2 Mb (ftp)(http) TSV
GSE84068_Supp_Table7_293_Let7_fit_hmm.tsv.gz 3.0 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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