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Sample GSM355924 Query DataSets for GSM355924
Status Public on Feb 28, 2013
Title SLAM Project Data: Synthetic Lethality with rrf1
Sample type genomic
 
Channel 1
Source name Reference
Organism Saccharomyces cerevisiae
Characteristics query gene: RRF1 (YHR038W, SGD ID S000001080)
knockout clone: Plate 217 well D07 (strain 21001)
genetic background: BY4743 (from S288C)
pool genotype: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX
Growth protocol Cells were grown at 30 degrees C for approximately eight doublings using "Magic Marker" selectable medium supplemented with uracil.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by phenol extraction or by use of proprietary kits (e.g., Epicentre, Norgen).
Label Cy5
Label protocol UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers.
 
Channel 2
Source name Test
Organism Saccharomyces cerevisiae
Characteristics query gene: RRF1 (YHR038W, SGD ID S000001080)
knockout clone: Plate 217 well D07 (strain 21001)
genetic background: BY4743 (from S288C)
pool genotype: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX
Growth protocol Cells were grown without added uracil, using materials and procedures that were otherwise the same as those for Channel 1.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by phenol extraction or by use of proprietary kits (e.g., Epicentre, Norgen).
Label Cy3
Label protocol UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers.
 
 
Hybridization protocol Labeled extracts were hybridized overnight to Agilent 22k microarray slides at 42 degrees C.
Scan protocol Images were acquired with a GenePix 4000B or 4200 AL scanner at 10 um resolution.
Description Internal identifier for dataset: SL/070711/14
Original datafile name: 070711_217_D07_14.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.431
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.35 1.68 1.86
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).
Data processing Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 5.1 or higher). Annotations were reconstructed from data downloaded from the Saccharomyces Genome Database on 2008-11-15. Numerical data were obtained as the median of foreground signal intensities. Background signal intensities were not used. Custom R packages (hoptag v3.9-7; hoptagInfo02A v3.9-6) were used with their default options. See the software and PDF documentation included with this GEO Series submission for details. The VALUE column represents a dynamically weighted sum of data from the UpTag and DnTag probes for each gene.
 
Submission date Dec 24, 2008
Last update date Feb 28, 2013
Contact name Jef Boeke
Organization name Johns Hopkins U
Street address 733 N BROADWAY # 339
City Baltimore
ZIP/Postal code 21205
Country USA
 
Platform ID GPL7872
Series (1)
GSE14217 Synthetic Lethality (SLAM) Project Data

Data table header descriptions
ID_REF Platform feature ID, representing a unique gene
VALUE Variance-stabilized log2 ratio (F532/F635)
WEIGHT Relative quality of data represented by VALUE
KAPPA Relative quantity of data summarized as VALUE
FLAG Indicator of outliers in VALUE (LOW or HIGH)

Data table
ID_REF VALUE WEIGHT KAPPA FLAG
1 -1.000 0.933 0.389
2 -0.186 1.000 0.389
3
4 -0.305 0.998 0.389
5 0.752 0.989 0.389
6 1.276 0.974 0.389
7 -0.863 0.998 0.389
8 0.152 1.000 0.389
9 -0.784 0.993 0.389
10 -0.610 0.853 0.389
11 0.587 0.975 0.611
12
13 1.570 0.995 0.389 HIGH
14 -0.057 1.000 0.389
15
16 0.183 1.000 0.389
17 0.059 1.000 0.389
18 0.089 0.947 0.389
19 0.210 1.000 0.389
20 -0.732 0.998 0.389

Total number of rows: 5868

Table truncated, full table size 121 Kbytes.




Supplementary file Size Download File type/resource
GSM355924.gpr.gz 2.0 Mb (ftp)(http) GPR
GSM355924_image.tif.gz 27.9 Mb (ftp)(http) TIFF
GSM355924_noDNA.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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