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Sample GSM611319 Query DataSets for GSM611319
Status Public on Oct 20, 2011
Title Candida tenuis Glucose Replicate 3
Sample type mixed
 
Channel 1
Source name Candida tenuis NRRL Y-1498 glucose
Organism Yamadazyma tenuis ATCC 10573
Characteristics treatment: 2% glucose for 3 generations growth
Treatment protocol One culture was treated with 2% glucose for 3 generations growth; the other culture was treated with 2% xylose for 3 generations growth.
Growth protocol Candida tenuis NRRL Y-1498 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase. Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures. Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture. Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.
Extracted molecule total RNA
Extraction protocol Cell collection, lysis, and total RNA isolation were performed as previously described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414. Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen). RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).
Label Cy5
Label protocol Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion). RNA collected from cells grown in each sugar condition was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.
 
Channel 2
Source name Candida tenuis NRRL Y-1498 genomic
Organism Yamadazyma tenuis ATCC 10573
Characteristics treatment: Genomic DNA was extracted from cells growing in log phase
Treatment protocol One culture was treated with 2% glucose for 3 generations growth; the other culture was treated with 2% xylose for 3 generations growth.
Growth protocol Candida tenuis NRRL Y-1498 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase. Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures. Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture. Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.
Extracted molecule genomic DNA
Extraction protocol Cell collection, lysis, and total RNA isolation were performed as previously described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414. Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen). RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).
Label Cy3
Label protocol Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion). RNA collected from cells grown in each sugar condition was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.
 
 
Hybridization protocol Arrays were hybridized in a NimbleGen hybridization system 12 (BioMicro) following the standard NimbleGen operating protocol. See www.nimblegen.com.
Scan protocol Arrays were scanned using a GenePix 4000B scanning laser (Molecular Devices) following the standard NimbleGen operating protocol. See www.nimblegen.com.
Description Biological replicate 3 of 3. Control glucose-grown cells, harvested after 3 generations.
Data processing Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al. (2004) Genome Biol 5: R80). The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3). Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF. See the included file CtenProbeMapping.txt for a mapping of probes to genes.
 
Submission date Oct 21, 2010
Last update date Oct 20, 2011
Contact name Dana Jasmine Wohlbach
E-mail(s) wohlbacd@dickinson.edu
Organization name Dickinson College
Department Biology
Street address P.O. Box 1773
City Carlisle
State/province PA
ZIP/Postal code 17013
Country USA
 
Platform ID GPL11082
Series (2)
GSE24856 Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose
GSE24858 Expression analysis of various fungi grown in glucose or xylose

Data table header descriptions
ID_REF
VALUE Quantile-normalized, averaged, log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
95710 2.996306
102379 -1.260318167
108050 -1.183540167
96716 -1.4623205
102422 -0.242323
108503 -1.269914667
109858 -1.293534833
110941 -2.6574075
100590 -1.307663833
100984 1.307323167
108920 -0.714301333
94932 0.643938167
109134 -1.016518667
109008 -2.654024833
98644 -0.2107625
96069 0.572021667
109096 0.157512667
98532 -1.990368
108585 -1.394111167
95235 3.6412525

Total number of rows: 5452

Table truncated, full table size 97 Kbytes.




Supplementary file Size Download File type/resource
GSM611319_Cten-GR3-327683.ftr.gz 8.5 Mb (ftp)(http) FTR
Processed data included within Sample table

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