|
| Status |
Public on Feb 28, 2013 |
| Title |
SLAM Project Data: Synthetic Lethality with oaz1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Reference
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
query gene: OAZ1 (YPL052W, SGD ID S000005973)
knockout clone: Plate 230 well A04 (strain 22776)
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: OAZ1 (YPL052W, SGD ID S000005973)
knockout clone: Plate 230 well A04 (strain 22776)
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 NimbleGen 72k 4-plex microarray slides at 42 degrees C.
|
| Scan protocol |
Images were acquired with a GenePix 4200AL scanner at 5 um resolution or an Agilent G2505C scanner at 2 um resolution
|
| Description |
Internal identifier for dataset: SL/100413/18
Original datafile name: 308500A02_532.pair
Original datafile2 name: 308500A02_635.pair
SD of values from reference genes: 0.520
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.83 1.22 1.76
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 NimbleScan software package (Roche NimbleGen, version 2.3.78 or higher). Annotations were reconstructed from data downloaded from the Saccharomyces Genome Database on 2008-11-15. Numerical data were obtained as the mean of the central pixels. Background signal intensities were not used. Custom R packages (hoptag v3.9-7; hoptagInfo07A 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 01, 2010 |
| 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 |
GPL7873 |
| Series (1) |
| GSE14217 |
Synthetic Lethality (SLAM) Project Data |
|
