|
| Status |
Public on Aug 11, 2017 |
| Title |
S15_bc_sc_rep2 |
| Sample type |
genomic |
| |
|
| Source name |
bc, sc
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
collection: bc
|
| Treatment protocol |
no drug
|
| Growth protocol |
Grown 5 generations in Sunrise Science Products SC-Met (cat#1343-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell pellets using YeastStar Genomic DNA Kit (Zymo Research, #D2002) and quantified using the NanoDrop 2000. Uptags and downtags were then PCR amplified using separate primers and 160ng of diluted genomic DNA with Phusion Hotstart.
|
| Label |
biotin
|
| Label protocol |
A biotin-labelling mix was made using 180uL 20xSSPE, 12uL 50x Denhardt's, 6ul 1% Tween 20, 1ul of 1mg/mL streptavidin-R-phycoerythrin congugate and 401uL ddH2O per sample. After priming the fluidics station, chips were stained with the biotin-labelling mix for approximately 30 minutes.
|
| |
|
| Hybridization protocol |
Each sample was hybridized for 16 hrs at 42 °C and 20 rpm with 60 uL of hybridization mix, as well as 30 uL of uptag and 30 uL of downtag PCR product. The hybridization mix consisted of 45uL 2x hybridization buffer, 0.3uL B213 control oligonucleotide (1fmol/uL), 7.2uL mixed oligonucleotide (12.5 pmol/uL), 1.8uL 50x Denhardt's. The 120uL sample/hyb mix was boiled for 2 minutes and iced for 2 minutes before loading onto a pre-treated Affymetrix chip.
|
| Scan protocol |
After the stain was removed and replaced with a wash buffer consisting of 6xSSPE, 0.01%Tween and H2O the chips were scanned immediately with the Affymetrix Scanner.
|
| Description |
Normalization Batch 1
|
| Data processing |
The raw data for uptags and downtags were normalized separately to the median of all arrays within a set (9 sets as defined by pool, media (SC), drug (YPD), or no growth (t0). Estimates of the background thresholds were determined independently for the control arrays in each set using Gaussian mixture models initialized on the unassigned tags on the control arrays.
|
| |
|
| Submission date |
Nov 10, 2016 |
| Last update date |
Aug 11, 2017 |
| Contact name |
Erica Acton |
| Organization name |
University of British Columbia
|
| Department |
Genome Science and Technology
|
| Lab |
Nislow/Giaever
|
| Street address |
Pharmaceutical Sciences Building, Wesbrook Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17030 |
| Series (1) |
| GSE89761 |
Genotype specific phenotypic behaviour of auxotrophic and prototrophic gene deletion collections |
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