 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 24, 2010 |
| Title |
Genome-wide Measurement of RNA Secondary Structure in Yeast |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
|
| |
|
| Overall design |
RNA sample was treated with one of two structure-specific enzymes (RNase V1 or RNase S1). Four independent V1 experiments and three independent S1 experiments were carried out.
Processed data file linked below. Data processing involves merging (or rather log-ratio-ing) the 7 lanes of SOLiD sequencing data against each other.
Also linked below are the genome and transcriptome FASTA files used for mapping, and the annotation file having the format: gene_ID, chromosome, start, end, feature. Start and end are 1-based; feature is "Transcript" for the entire transcript (including introns), "Intron", "Exon", "5UTR" or "3UTR".
Genome-wide measurement of RNA secondary structure in yeast, Kertesz et al., Nature Volume:467, Pages:103-107, Date published:(02 September 2010)
http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html
|
| |
|
| Contributor(s) |
Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E |
| Citation(s) |
20811459 |
| |
| Submission date |
Jun 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Kertesz |
| Organization name |
Stanford University
|
| Street address |
318 Campus Dr.
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL10577 |
AB SOLiD System (Saccharomyces cerevisiae) |
|
| Samples (7)
|
| GSM558924 |
Total RNA from yeast, treated with RNase V1, replicate 1 |
| GSM558925 |
Total RNA from yeast, treated with RNase V1, replicate 2 |
| GSM558926 |
Total RNA from yeast, treated with RNase V1, replicate 3 |
| GSM558927 |
Total RNA from yeast, treated with RNase V1, replicate 4 |
| GSM558928 |
Total RNA from yeast, treated with RNase S1, replicate 1 |
| GSM558929 |
Total RNA from yeast, treated with RNase S1, replicate 2 |
| GSM558930 |
Total RNA from yeast, treated with RNase S1, replicate 3 |
|
| Relations |
| SRA |
SRP003175 |
| BioProject |
PRJNA128665 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22393_processed_merged_PARS_sacCer2_1.wig.gz |
11.4 Mb |
(ftp)(http) |
WIG |
| GSE22393_sce_0608.fasta.gz |
3.3 Mb |
(ftp)(http) |
FASTA |
| GSE22393_sce_genes.fasta.gz |
1.3 Mb |
(ftp)(http) |
FASTA |
| GSE22393_sce_transcriptome_global.tab.gz |
92.7 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...