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Sample GSM1045053 Query DataSets for GSM1045053
Status Public on Nov 28, 2012
Title yal008w heterozygous diploid, Replicate 3
Sample type SRA
 
Source name yeast mRNA extract
Organism Saccharomyces cerevisiae
Characteristics strain background: BY4741
genotype/variation: yal008w heterozygous
Treatment protocol No treatment (conditions lack G418)
Growth protocol YPD; log-growth from OD 0.2 to 1.0 at 30*C.
Extracted molecule total RNA
Extraction protocol Hybrid Trizol Reagent RNA extraction and RNEAsy column purification
mRNA were purified via Oligo-DT dynabeads twice; purified mRNA were fragmented to yield fragments averaging 200-300-bp.Illumina adapters were then ligated and amplified, followed by size-selection and qPCR quantitation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Base-calling provided by Illumina stock software. Details on what is used by the UCSD core can be found at microarrays.ucsd.edu
Reads were aligned via Bowtie 0.12.5 with the following arguments (-m 1 -B 1)
Data were filtered to only accept non-clonal reads
Counts for each ORF were tallied as the median number of non-clonal reads overallping positions in the last 200 bases of each yeast ORF (Nagalakshmi, 2011)
Genome_build: scerevisiae genome downloaded from SGD in 06/2012
Supplementary_files_format_and_content: tab-delimited file contains a matrix with each row representing each yeast ORF and each column representing RNA-Seq measurements in each experiment. Each cell reports the number of counts observed in the corresponding experiment for the corresponding ORF.
 
Submission date Nov 27, 2012
Last update date May 15, 2019
Contact name Menzies Chen
E-mail(s) mec001@ucsd.edu
Organization name UCSD
Department Bioengineering
Lab Ideker Lab
Street address 9500 Gilman Drive MC 0688
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL13821
Series (1)
GSE42554 Decoupling epigenetic and genetic effects through systematic analysis of gene position
Relations
SRA SRX206569
BioSample SAMN01819941

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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