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Sample GSM1860424 Query DataSets for GSM1860424
Status Public on Apr 30, 2017
Title Barcoded PCA pool-yeast nitrogen base with heat-shock-biological rep 1
Sample type genomic
 
Source name barcoded PCA pool-3 generations yeast nitrogen base with heat-shock-biological rep 1
Organism Saccharomyces cerevisiae
Characteristics pool: barcoded protein-complementation assay strains
strain/background: S288c
growth stage: 3 generations
agent: yeast nitrogen base with heat
Treatment protocol FK506, CuSO4, doxorubicin, 1181-0519, atorvastatin, hydrogen peroxide, low concentration of ammonium sulfate, NaCl, Sorbitol, Menadione, High Temperature, complete synthetic amino acid mix, methionine were incorporated into growth media in the treatment samples.
Growth protocol Growth in minimal media (yeast nitrogen base and ammonium sulfate) supplemented with 2% of either glucose or 2% ethanol at 30 °C with vigorous shaking. Measurements of optical density at 595 nm (OD595) were used to monitor growth every 15 min. Samples were harvested after precisely 3 pool generations. CRISPRi samples were harvested after 10 generations.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from cell pellets using the YeaStar Genomic DNA kit from Zymo Research (D2002).
Label biotin
Label protocol The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers.
 
Hybridization protocol PCR reactions of up- and down-tags were mixed in equal volumes (30 ul each) and hybridized overnight to custom-built TAG4 microarrays (Affymetrix).
Scan protocol After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).
Description High-Temp.1
Barcoded PCA pool-3 generations yeast nitrogen base with heat-shock-biological rep 1.
Data processing All cells carry two tags that hybridize to the GenFlex tag 16k array, an uptag and a downtag. From each array, we extracted the fluorescence intensity values for every uptag and downtag associated with the 1383 strains in the bar-coded PCA pool. These raw fluorescence values were quantile-normalized and then log2-transformed using the normalize.quantiles function of the preprocessCore package in R. Quantile normalization was performed separately for uptags and downtags. Fourteen experimental conditions were measured in duplicate, and the control condition (DMSO) was measured with 6 replicates. The distance between the means (fold-change or FC) of the control condition and each experimental condition was calculated separately for uptags and downtags. A moderated t-statistic was then calculated using the R package LIMMA, and the derived p-values were further converted to q-values using Benjamini & Hochberg False Discovery Rate (FDR) correction using the p.adjust function in R. A separate q-value was calculated for uptags and downtags. PCA strains with a significant increase in their tag abundance in response to an experimental condition were identified using (q-value < 0.05 for both uptag and downtag) and FC > 0.25 (for both uptag and downtag) as cutoffs. PCA strains with a significant decrease in tag abundance were identified using (q-value < 0.05 for both uptag and downtag) and FC < -0.25 (for both uptag and downtag) as cutoffs.
 
Submission date Aug 24, 2015
Last update date Apr 30, 2017
Contact name Ulrich Schlecht
E-mail(s) schlecht.ulrich@gmail.com
Phone 6502136281
Organization name Stanford University
Department Biochemistry
Lab Ronald W. Davis
Street address 3165 Porter Drive
City Palo Alto
ZIP/Postal code 94304
Country USA
 
Platform ID GPL20845
Series (2)
GSE72336 Systematic identification of changes in the yeast protein interaction network in response to environmental, chemical, and genetic perturbation [interactome data]
GSE72425 Systematic identification of changes in the yeast protein interaction network in response to environmental, chemical, and genetic perturbation

Data table header descriptions
ID_REF
VALUE Log2-transformed quantile-normalized fluorescence units

Data table
ID_REF VALUE
TM_1345:uptag 11.79239378
TM_3728:uptag 11.10530289
TM_3802:uptag 11.17724822
TM_3747:uptag 11.88760142
TM_4013:uptag 10.88752527
TM_1337:uptag 11.87135662
TM_1133:uptag 12.03183041
TM_3886:uptag 12.04514533
TM_3805:uptag 11.47845365
TM_0659:uptag 11.57752324
TM_0764:uptag 11.54848479
TM_0017:uptag 12.32998549
TM_3596:uptag 11.60373065
TM_1358:uptag 10.96387145
TM_3321:uptag 11.61282243
TM_3185:uptag 11.3365484
TM_4056:uptag 11.38724998
TM_0144:uptag 12.3016248
TM_3992:uptag 11.93449254
TM_1644:uptag 11.53480137

Total number of rows: 2766

Table truncated, full table size 72 Kbytes.




Supplementary file Size Download File type/resource
GSM1860424_14_02_27_U49.CEL.gz 581.3 Kb (ftp)(http) CEL
Processed data included within Sample table

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