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Sample GSM1387087 Query DataSets for GSM1387087
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
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
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
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
BioSample SAMN02781052
SRA SRX543755

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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