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Sample GSM2388161 Query DataSets for GSM2388161
Status Public on Aug 11, 2017
Title S17_bc_ura_rep2
Sample type genomic
 
Source name bc, sc-ura
Organism Saccharomyces cerevisiae
Characteristics collection: bc
Treatment protocol no drug
Growth protocol Grown 5 generations in Sunrise Science Products SC-Ura (cat#1306-030)
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

Data table header descriptions
ID_REF
VALUE Median normalized signal intensity.

Data table
ID_REF VALUE
YAL002W::chr1_1:uptag 6.1154
YAL004W::chr1_1:uptag 9.0153
YAL005C::chr1_1:uptag 10.2449
YAL007C::chr1_1:uptag 6.9216
YAL008W::chr1_1:uptag 7.6484
YAL009W::chr1_1:uptag 6.0745
YAL010C::chr1_1:uptag 6.0662
YAL011W::chr1_1:uptag 10.4378
YAL012W::chr00_12:downtag 9.5975
YAL012W::chr00_12:uptag 9.5814
YAL013W::chr1_1:uptag 9.2053
YAL014C::chr1_1:uptag 9.6869
YAL015C::chr1_1:uptag 10.6926
YAL016C-B::chr00_20:downtag 11.5946
YAL016C-B::chr00_20:uptag 6.261
YAL016W::chr00_12:downtag 5.938
YAL016W::chr00_12:uptag 6.6428
YAL017W::chr1_1:uptag 10.6774
YAL018C::chr1_1:uptag 9.621
YAL019W::chr1_1:uptag 7.2463

Total number of rows: 10216

Table truncated, full table size 310 Kbytes.




Supplementary file Size Download File type/resource
GSM2388161_51133100740806020117425556791700.CEL.gz 329.8 Kb (ftp)(http) CEL
Processed data included within Sample table

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