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Series GSE25028

Query DataSets for GSE25028

Status

Public on Dec 04, 2010

Title

[E-MTAB-305] ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification

Organism

Homo sapiens

Experiment type

Non-coding RNA profiling by high throughput sequencing

Summary

ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification
Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available.

ArrayExpress Release Date: 2010-07-05

Publication Title: ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification
Publication Author List: Matthew Biery,Heather Bouzek,Ronghua Chen,Stuart Jackson,Jason M. Johnson,Carol A. Rohl,Chris K. Raymond,David Haynor,Christopher D. Armour,John C. Castle

Person Roles: submitter
Person Last Name: Loewer
Person First Name: Martin
Person Mid Initials:
Person Email: martin.loewer@tron-mainz.de
Person Phone: +49 6131-720298-11
Person Address: TRON Translationale Onkologie gGmbH, Langenbeckstr. 8, D-55131 Mainz
Person Affiliation: TRON

Overall design

Experimental Design: organism_part_comparison_design
Experimental Design: all_pairs
Experimental Design: transcription profiling by high throughput sequencing
Experimental Factor Name: ORGANISMPART
Experimental Factor Type: organism_part

Citation(s)

20668672

Submission date

Oct 29, 2010

Last update date

May 15, 2019

Organization

European Bioinformatics Institute

E-mail(s)

miamexpress@ebi.ac.uk

Lab

ArrayExpress