|
| Status |
Public on Feb 05, 2011 |
| Title |
[E-MTAB-5] Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and many functional properties of transcripts are not based on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. This transcriptional complexity has been sampled mainly using hybridization-based methods under one or a few conditions. We applied direct high-throughput sequencing of cDNAs, complemented with different expression data from high-density tiling arrays, to globally sample transcripts of the fission yeast Schizosaccharomyces pombe, independently from available gene annotations. We interrogated transcriptomes under multiple conditions, including exponential proliferation, meiotic differentiation and environmental stress, and in RNA processing mutants, to reveal the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental, and genetic factors. High-throughput sequencing proved to be a powerful and quantitative method to deeply sample transcriptomes at unprecedented resolution. Unlike hybridization, sequencing showed little, if any, background noise and was sensitive enough to detect widespread transcription in >90% of the genome, including traces of RNAs that were not actively transcribed or rapidly degraded. The combined sequencing and strand-specific array data provided rich information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus refining the existing genome annotation. Sequence trans-reads spanning exon-exon or exon-intron junctions gave unique insight into a surprising variability in splicing efficiency across introns and genes. Splicing efficiency was largely coordinated with transcriptional efficiency, and hundreds of introns showed regulated splicing as a function of cellular proliferation or differentiation.
ArrayExpress Release Date: 2008-12-03
Publication Title: Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution
Publication Author List: Brian Wilhelm, Samuel Marguerat, Stephen Watt, Falk Schubert, Valerie Wood, Ian Goodhead, Christopher J. Penkett, Jane Rogers and Jurg Bahler
Person Roles: submitter
Person Last Name: Wilhelm
Person First Name: Brian
Person Mid Initials:
Person Email: btw@sanger.ac.uk
Person Phone:
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Person Affiliation: Wellcome Trust Sanger Institute
Person Roles: investigator
Person Last Name: Bahler
Person First Name: Jurg
Person Mid Initials
Person Email: jurg@sanger.ac.uk
Person Phone
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Person Affiliation: Wellcome Trust Sanger Institute
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| |
|
| Overall design |
Experimental Design: growth_condition_design
Experimental Design: replicate_design
Experimental Design: co-expression_design
Experimental Factor Name: MEDIA
Experimental Factor Name: TIME
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Name: TEMPERATURE
Experimental Factor Name: CULTURE_DENSITY
Experimental Factor Type: media
Experimental Factor Type: time
Experimental Factor Type: growth_condition
Experimental Factor Type: temperature
Experimental Factor Type: culture_density
Quality Control Type: biological_replicate
|
| |
|
| Citation(s) |
18488015 |
| |
| Submission date |
Oct 28, 2010 |
| Last update date |
Mar 26, 2012 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL9854 |
Illumina Genome Analyzer (Schizosaccharomyces pombe) |
|
| Samples (31)
|
|
| Relations |
| ArrayExpress |
E-MTAB-5 |
| BioProject |
PRJNA134361 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE25003_normM01_solexa_logscore_Rchrm1.txt.gz |
17.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM01_solexa_logscore_Rchrm2.txt.gz |
14.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM01_solexa_logscore_Rchrm3.txt.gz |
7.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM02_solexa_logscore_Rchrm1.txt.gz |
18.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM02_solexa_logscore_Rchrm2.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM02_solexa_logscore_Rchrm3.txt.gz |
7.9 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM03_solexa_logscore_Rchrm1.txt.gz |
18.1 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM03_solexa_logscore_Rchrm2.txt.gz |
14.7 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM03_solexa_logscore_Rchrm3.txt.gz |
8.0 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM11_solexa_logscore_Rchrm1.txt.gz |
17.8 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM11_solexa_logscore_Rchrm2.txt.gz |
14.5 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM11_solexa_logscore_Rchrm3.txt.gz |
7.7 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM12_solexa_logscore_Rchrm1.txt.gz |
18.4 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM12_solexa_logscore_Rchrm2.txt.gz |
14.9 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM12_solexa_logscore_Rchrm3.txt.gz |
8.0 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM13_solexa_logscore_Rchrm1.txt.gz |
18.4 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM13_solexa_logscore_Rchrm2.txt.gz |
15.0 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM13_solexa_logscore_Rchrm3.txt.gz |
8.1 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM21_solexa_logscore_Rchrm1.txt.gz |
17.5 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM21_solexa_logscore_Rchrm2.txt.gz |
14.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM21_solexa_logscore_Rchrm3.txt.gz |
7.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM22_solexa_logscore_Rchrm1.txt.gz |
18.0 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM22_solexa_logscore_Rchrm2.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM22_solexa_logscore_Rchrm3.txt.gz |
7.8 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM23_solexa_logscore_Rchrm1.txt.gz |
18.0 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM23_solexa_logscore_Rchrm2.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM23_solexa_logscore_Rchrm3.txt.gz |
7.9 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM31_solexa_logscore_Rchrm1.txt.gz |
17.1 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM31_solexa_logscore_Rchrm2.txt.gz |
13.8 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM31_solexa_logscore_Rchrm3.txt.gz |
7.4 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM32_solexa_logscore_Rchrm1.txt.gz |
17.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM32_solexa_logscore_Rchrm2.txt.gz |
14.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM32_solexa_logscore_Rchrm3.txt.gz |
7.7 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM33_solexa_logscore_Rchrm1.txt.gz |
17.5 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM33_solexa_logscore_Rchrm2.txt.gz |
14.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM33_solexa_logscore_Rchrm3.txt.gz |
7.8 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM41_solexa_logscore_Rchrm1.txt.gz |
15.9 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM41_solexa_logscore_Rchrm2.txt.gz |
12.9 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM41_solexa_logscore_Rchrm3.txt.gz |
7.0 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM42_solexa_logscore_Rchrm1.txt.gz |
16.3 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM42_solexa_logscore_Rchrm2.txt.gz |
13.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM42_solexa_logscore_Rchrm3.txt.gz |
7.2 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM43_solexa_logscore_Rchrm1.txt.gz |
16.4 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM43_solexa_logscore_Rchrm2.txt.gz |
13.3 Mb |
(ftp)(http) |
TXT |
| GSE25003_normM43_solexa_logscore_Rchrm3.txt.gz |
7.3 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set1_solexa_logscore_Rchrm1.txt.gz |
18.1 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set1_solexa_logscore_Rchrm2.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set1_solexa_logscore_Rchrm3.txt.gz |
7.8 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set2_solexa_logscore_Rchrm1.txt.gz |
19.7 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set2_solexa_logscore_Rchrm2.txt.gz |
15.8 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set2_solexa_logscore_Rchrm3.txt.gz |
8.4 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set3_solexa_logscore_Rchrm1.txt.gz |
19.9 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set3_solexa_logscore_Rchrm2.txt.gz |
16.1 Mb |
(ftp)(http) |
TXT |
| GSE25003_norm_filtered_wt_current_Set3_solexa_logscore_Rchrm3.txt.gz |
8.7 Mb |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data are available on Series record |
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