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Sample GSM1365918 Query DataSets for GSM1365918
Status Public on Jul 28, 2014
Title BY-Ribo_logphase_Replicate1
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 strain BY4741 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:Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-BY4741-Ribosome Occupancy Fold Change: RNA-Glu/RNA+Glu(log2)-EY0690-mRNA Fold Change: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-EY0690-Ribosome Occupancy Fold Change: Ribo+Glu_InitiationRegion-BY4741: Ribo+Glu_DownstreamRegion-BY4741: Ribo-Glu_InitiationRegion-BY4741: Ribo-Glu_DownstreamRegion-BY4741: RNA+Glu_InitiationRegion-BY4741_TotalRNA: RNA+Glu_DownstreamRegion-BY4741_TotalRNA: RNA-Glu_InitiationRegion-BY4741_TotalRNA: RNA-Glu_DownstreamRegion-BY4741_TotalRNA: Ribo+Glu_InitiationRegion-EY0690: Ribo+Glu_DownstreamRegion-EY0690: Ribo-Glu_InitiationRegion-EY0690: Ribo-Glu_DownstreamRegion-EY0690: RNA+Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA: RNA+Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA: RNA-Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA: RNA-Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA: Ribo+Glu_RPKM-BY4741: Ribo-Glu_RPKM-BY4741: RNA+Glu_RPKM-BY4741: RNA-Glu_RPKM-BY4741: Ribo+Glu_RPKM-EY0690: Ribo-Glu_RPKM-EY0690: RNA+Glu_RPKM-EY0690: RNA-Glu_RPKM-EY0690
 
Submission date Apr 08, 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 SAMN02721676
SRA SRX513393

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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