|
| Status |
Public on Jul 28, 2014 |
| Title |
BY-Ribo_logphase_Replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast BY4741
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
strategy: Ribosome Profiling
treatment: +Glucose
|
| Treatment protocol |
All samples were treated for 1 min with cycloheximide 100ug/ml
|
| Growth protocol |
Yeast strains BY4741 and EY0690 (w303) was grown at 30C in synthetic complete + glucose media to OD600 =0.3-0.4. Then 15min into SC -glucose media as indicated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Footprints: cells were rapidly harvested, flash-frozen in polysome lysis buffer, and pulverized in a mixer mill, extracts were digested with 100 U Rnase I for 30 min, monosomes were purified by sucrose density gradient or by sucrose cushion, RNA was extracted from the monosome fraction by hot acid phenol; total RNA was prepared from flash-frozen cells by the hot acid phenol protocol, polyA RNA was purified by oligo-dT DynaBeads, or RiboZero selected RNA or Total RNA, and fragmented at 95 C under mild alkali conditions
Libraries were prepared by polyA tailing 28mers followed by reverese transcription with either OTi225 or OTi9pA, see Methods in Zid et al, in submission
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Ribosome protected mRNA
+Glucose
|
| Data processing |
Reads were trimmed of their polyA tail and then aligned to the S. cerevisiae genome using Bowtie-0.12.8.
Reads were aligned to a library of RNA genes
Remaining reads were aligned to the S. cerevisiae genome R64-1-1
Genome_build: http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz
Supplementary_files_format_and_content: Each line in the tab deliminated txt file has the following columns: Systematic Name: Name: Descript: Start: End: Length: RNA-Glu/RNA+Glu(log2)-BY4741-mRNA Fold Change Replicate 1: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 1: RNA-Glu/RNA+Glu(log2)-EY0690-mRNA Fold Change Replicate 1: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-BY4741-mRNA Fold Change Replicate 1: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-BY4741-mRNA Fold Change Replicate 2: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 2: RNA(pA)-Glu/RNA(pA)+Glu(log2)-EY0690-mRNA Fold Change Replicate 1: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-EY0690-mRNA Fold Change Replicate 2: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 2: Ribo+Glu_RPKM-BY4741 - Replicate 1: Ribo-Glu_RPKM-BY4741 - Replicate 1: RNA+Glu_RPKM-BY4741 TotalRNA - Replicate 1: RNA-Glu_RPKM-BY4741 TotalRNA - Replicate 1: Ribo+Glu_RPKM-EY0690 - Replicate 1: Ribo-Glu_RPKM-EY0690 - Replicate 1: RNA+Glu_RPKM-EY0690 TotalRNA - Replicate 1: RNA-Glu_RPKM-EY0690 TotalRNA - Replicate 1: RNA+Glu_RPKM-BY4741 polyA_RNA - Replicate 1: RNA-Glu_RPKM-BY4741 polyA_RNA - Replicate 1: Ribo+Glu_RPKM-BY4741 - Replicate 2: Ribo-Glu_RPKM-BY4741 - Replicate 2: RNA+Glu_RPKM-BY4741 polyA_RNA - Replicate 2: RNA-Glu_RPKM-BY4741 polyA_RNA - Replicate 2: RNA+Glu_RPKM-EY0690 polyA_RNA - Replicate 1: RNA-Glu_RPKM-EY0690 polyA_RNA - Replicate 1: Ribo+Glu_RPKM-EY0690 - Replicate 2: Ribo-Glu_RPKM-EY0690 - Replicate 2: RNA+Glu_RPKM-EY0690 polyA_RNA - Replicate 2: RNA-Glu_RPKM-EY0690 polyA_RNA - Replicate 2: Ribo+Glu_InitiationRegion-BY4741 Replicate 1: Ribo+Glu_DownstreamRegion-BY4741 Replicate 1: Ribo-Glu_InitiationRegion-BY4741 Replicate 1: Ribo-Glu_DownstreamRegion-BY4741 Replicate 1: RNA+Glu_InitiationRegion-BY4741_TotalRNA Replicate 1: RNA+Glu_DownstreamRegion-BY4741_TotalRNA Replicate 1: RNA-Glu_InitiationRegion-BY4741_TotalRNA Replicate 1: RNA-Glu_DownstreamRegion-BY4741_TotalRNA Replicate 1: Ribo+Glu_InitiationRegion-EY0690 Replicate 1: Ribo+Glu_DownstreamRegion-EY0690 Replicate 1: Ribo-Glu_InitiationRegion-EY0690 Replicate 1: Ribo-Glu_DownstreamRegion-EY0690 Replicate 1: RNA+Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA+Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA-Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA-Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA+Glu_InitiationRegion-BY4741_polyA_RNA Replicate 1: RNA+Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 1: RNA-Glu_InitiationRegion-BY4741_polyA_RNA Replicate 1: RNA-Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 1: Ribo+Glu_InitiationRegion-BY4741 Replicate 2: Ribo+Glu_DownstreamRegion-BY4741 Replicate 2: Ribo-Glu_InitiationRegion-BY4741 Replicate 2: Ribo-Glu_DownstreamRegion-BY4741 Replicate 2: RNA+Glu_InitiationRegion-BY4741_polyA_RNA Replicate 2: RNA+Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 2: RNA-Glu_InitiationRegion-BY4741_polyA_RNA Replicate 2: RNA-Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 2: RNA+Glu_InitiationRegion-EY0690_polyA_RNA Replicate 1: RNA+Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 1: RNA-Glu_InitiationRegion-EY0690_polyA_RNA Replicate 1: RNA-Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 1: Ribo+Glu_InitiationRegion-EY0690 Replicate 2: Ribo+Glu_DownstreamRegion-EY0690 Replicate 2: Ribo-Glu_InitiationRegion-EY0690 Replicate 2: Ribo-Glu_DownstreamRegion-EY0690 Replicate 2: RNA+Glu_InitiationRegion-EY0690_polyA_RNA Replicate 2: RNA+Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 2: RNA-Glu_InitiationRegion-EY0690_polyA_RNA Replicate 2: RNA-Glu_DownstreamRegion-EY0690_polyA_RNA Replicate
|
| |
|
| Submission date |
May 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Matthew Zid |
| E-mail(s) |
zid@ucsd.edu
|
| Organization name |
University of California San Diego
|
| Department |
Chemistry and Biochemistry
|
| Lab |
Zid
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (1) |
| GSE56622 |
Ribosome profiling upon glucose starvation in S. cerevisiae |
|
| Relations |
| BioSample |
SAMN02781052 |
| SRA |
SRX543755 |
