A set of 5,908 69-70 mers oligonucleotides that correspond to all C. glabrata putative open reading frames and some non-coding sequences was designed and synthesized at Pasteur Institute, France. Each oilgonucleotide was dissolved into 50% DMSO and spotted on UltraGAPsTM glass slides (Corning Incorporated, Acton, MA) in duplicate to generate whole genome microarray for C. glabrata. The microarray was printed at Biotechnology Research Institute/National Research Council of Canada in Montreal. The sequence information of the oligonucleotides and the micorarray setup can be found at platform GPL3922. Using the microarray, the transcriptional profiles of C. glabrata cells that were coincubated with J774A.1 murine Macrophage-like cells for 2 and 6 hrs were examined. At each time point, three biological repeats were done. 20 ug of total RNA from either macrophage-ingested C. glabrata cells (experimental sample) or the medium-alone controls (control sample) was used to synthesize Cy5- or Cy3-labeled cDNA probes with an anchor primer [(dT)18(dA/dG/dC)] in the presence of Cy5- or Cy3-dCTP (PerkinElmer). For each pair of experimental and control samples, dye-swap was performed, that is, two probe mixtures, the Cy5-experimental plus the Cy3-control probes, and conversely, the Cy3-experimental plus the Cy5-control probes were individually hybridized with a single C. glabrata microarray slide. The hybridization and subsequent washing conditions follows the instruction on the manual for UltraGAPsTM glass slides. The hybridized microarrays were scanned with Axon 4000B scanner, and Data were extracted using Axon GenePix program. Log2 (experimental/control) for each spot on the microarray was calculated. From each dye-swap experiment, the Log2 (experimental / control) for each spot were averaged. Finally, 6 Log2 (experimental/control) values (3 repeats × duplicate spots on each slide) were imported into SAM (significance analysis of microarrays) software for statistical analysis. For genes that are considered significantly induced or repressed, the median of false discovery rate (FDR) equals to 0, while the 90% FDR is less than 0.001. Keywords: transcriptional profiling by microarray
Overall design
GSM140373 and GSM140374 are dye-swap experiment #1 for hour 2 time point; GSM140375 and GSM140621 are dye-swap experiment #2 for hour 2 time point; GSM140625 and GSM140626 are dye-swap experiment #3 for hour 2 time point. GSM140627 and GSM140631 are dye-swap experiment #1 for hour 6 time point; GSM140632 and GSM140633 are dye-swap experiment #2 for hour 6 time point; GSM140634 and GSM140635 are dye-swap experiment #3 for hour 6 time point.
Table 1: C. glabrata genes induced at least 2 fold after infecting murine macrophage-like cell J774A for 2 and 6 hours (Genes significantly induced at both hour 2 and hour 6, ** Values are not statistically significant from 3 independent transcriptional profiling experiment) header descriptions
C.g. Gene ID
(Macrophage/Control) hr 2
(Macrophage/Control) hr 6
Homologue in S.cerevisiae
Gene
Biological process
Function
Data table
C.g. Gene ID
(Macrophage/Control) hr 2
(Macrophage/Control) hr 6
Homologue in S.cerevisiae
Gene
Biological process
Function
CAGL0F00209g
98.33
28.44
YGR260W-like
TNA1-like
putative transporter, substrate unknown
CAGL0M03465g
83.52
18.57
YCR010C
ADY2
meiosis*
ammonium transporter activity*
CAGL0L09086g
80.09
10.21
YPR001W
CIT3
tricarboxylic acid cycle*
citrate (Si)-synthase activity
CAGL0L09108g
74.05
12.58
YPR002W
PDH1
propionate metabolism
molecular function unknown
CAGL0G02739g
65.34
7.34
YIL101C
XBP1
response to stress
transcription factor activity
CAGL0H06633g
64.65
21.38
YKR097W
PCK1
gluconeogenesis
phosphoenolpyruvate carboxykinase (ATP) activity
CAGL0E05984g
57.18
20.86
YMR173W
DDR48
DNA repair
ATPase activity*
CAGL0L00649g
54.01
7.46
YAL054C
ACS1
acetyl-CoA biosynthesis*
acetate-CoA ligase activity
CAGL0H09460g
47.87
3.9
YER015W
FAA2
lipid metabolism*
long-chain-fatty-acid-CoA ligase activity
CAGL0K10868g
35.83
4.61
YDR256C
CTA1
oxygen and reactive oxygen species metabolism
catalase activity
CAGL0L03267g
34.91
8.5
YKR039W
GAP1
amino acid transport*
L-proline permease activity*
CAGL0G05269g
34.26
10.26
YDR070C
FMP16
biological process unknown
molecular function unknown
CAGL0J03058g
30.32
8.81
YER065C
ICL1
glyoxylate cycle
isocitrate lyase activity
CAGL0L02167g
30.16
3.05
YKR009C
FOX2
fatty acid beta-oxidation
3-hydroxyacyl-CoA dehydrogenase activity*
CAGL0C05027g
24.68
8.49
YAR035W
YAT1
alcohol metabolism*
carnitine O-acetyltransferase activity
CAGL0L09273g
24.29
5.68
YPR006C
ICL2
propionate metabolism*
methylisocitrate lyase activity
CAGL0I02134g
19.43
4.02
YGR239C
PEX21
protein targeting to peroxisome
protein binding*
CAGL0D00154g
18.96
3.4
YPR192W
AQY1
sporulation (sensu Fungi)*
water channel activity
CAGL0H06787g
18.88
4.02
YIL160C
POT1
fatty acid beta-oxidation
acetyl-CoA C-acyltransferase activity
CAGL0H04939g
18.76
9.14
YLR377C
FBP1
gluconeogenesis
fructose-bisphosphatase activity
Total number of rows: 326
Table truncated, full table size 29 Kbytes.
Table 2: C. glabrata genes repressed at least 2 fold after infecting murine macrophage-like cell J774A for 2 and 6 hours (Genes significantly repressed at both hour 2 and hour 6, ** Values are not statistically significant from 3 independent transcriptional profiling experiment) header descriptions
C.g. Gene ID
(Macrophage/Control) hr 2
(Macrophage/Control) hr 6
Homologue in S.cerevisiae
Gene
Biological process
Function
Data table
C.g. Gene ID
(Macrophage/Control) hr 2
(Macrophage/Control) hr 6
Homologue in S.cerevisiae
Gene
Biological process
Function
CAGL0J09944g
0.045
0.353
YNL065W
AQR1
drug transport*
monocarboxylic acid transporter activity*
CAGL0B00990g
0.052
0.06
YCL026C-B
biological process unknown
molecular function unknown
CAGL0A01540g
0.058
0.34
YGL030W
RPL30
translation*
structural constituent of ribosome
CAGL0J07238g
0.06
0.314
YOR369C
RPS12
translation
structural constituent of ribosome
CAGL0F07073g
0.062
0.332
YGL123W
RPS2
translation*
structural constituent of ribosome
CAGL0A01782g
0.064
0.106
YDR343C
HXT6
hexose transport
glucose transporter activity*
CAGL0D02090g
0.064
0.378
YMR116C
ASC1
telomere maintenance*
molecular function unknown
CAGL0E04092g
0.065
0.236
YHL040C
ARN1
siderophore-iron transport
siderophore-iron transporter activity
CAGL0K03135g
0.068
0.281
YHL015W
RPS20
translation
structural constituent of ribosome
CAGL0K07414g
0.068
0.287
YOR312C
RPL20B
translation*
structural constituent of ribosome
CAGL0G07227g
0.069
0.305
YML026C
RPS18B
translation
structural constituent of ribosome
CAGL0G05940g
0.07
0.325
YNL162W
RPL42A
translation
structural constituent of ribosome
CAGL0E04994g
0.071
0.401
YNL067W
RPL9B
translation
structural constituent of ribosome
CAGL0M06523g
0.075
0.326
YBR191W
RPL21A
translation*
structural constituent of ribosome
CAGL0A04521g
0.078
0.36
YER102W
RPS8B
translation
structural constituent of ribosome
CAGL0F02937g
0.078
0.352
YEL054C
RPL12A
translation*
structural constituent of ribosome
CAGL0J00165g
0.078
0.323
YLR333C
RPS25B
translation
structural constituent of ribosome
CAGL0G08734g
0.078
0.372
YNL067W
RPL9B
translation
structural constituent of ribosome
CAGL0G03575g
0.079
0.34
YER117W
RPL23B
translation
structural constituent of ribosome
CAGL0M02849g
0.08
0.361
YLR048W
RPS0B
translation*
structural constituent of ribosome
Total number of rows: 725
Table truncated, full table size 67 Kbytes.
Table 3: The transcription profile of all genes in C. glabrata cells co-incubate with J774.1 murine macrophages for 2 hours (analyzed by SAM 2.0 software) header descriptions
Oligo ID
ID of each oligonucleotide used on microarray
ORF Name
Name of open reading frame corresponding to each oligonucleotide on the microarray
Score(d)
The T-statistic value calculated by SAM 2.0 software (The higher the absolute value of the Score, the more significant of a given transcript)
Macrophage/control (hr 2)
The average ratio of the level of a given transcript in yeast cells co-incubated with macrophages for 2 hrs versus in cells grown in medium alone for 2 hrs
Denominator(s+s0)
Denominator of the T-statistics
q-value(%)
The lowest false discovery rate of each given transcript
local fdr(%)
Local false discovery rate of each given transcript
Data table
Oligo ID
ORF Name
Score(d)
Macrophage/control (hr 2)
Denominator(s+s0)
q-value(%)
local fdr(%)
3809.1-1054-1123
CAGL0F00209g
7.71
98.33
0.86
0
0
7484.1-1034-1103
CAGL0L09086g
6.66
80.09
0.95
0
0
7483.1-1107-1176
CAGL0L09108g
6.55
74.05
0.95
0
0
5688.1-76-145
CAGL0G05269g
6.37
34.26
0.8
0
0
3588.2-1293-1362
CAGL0G02739g
6.26
65.34
0.96
0
0
6814.1-147-217
CAGL0M03465g
6.01
83.52
1.06
0
0.01
2728.1-1105-1174
CAGL0L03267g
5.52
34.91
0.93
0
0.04
72.1-1937-2006
CAGL0H09460g
5.47
47.87
1.02
0
0.04
7519.1-1947-2015
CAGL0L00649g
5.47
54.01
1.05
0
0.04
4109.1-1452-1521
CAGL0C05027g
5.17
24.68
0.9
0
0.07
8437.1-1857-1926
CAGL0L02167g
5.08
30.16
0.97
0
0.07
290.1-1526-1595
CAGL0H06633g
5.01
64.65
1.2
0
0.08
3249.1-515-584
CAGL0K10868g
4.92
35.83
1.05
0
0.08
6022.1-150-219
CAGL0E05984g
4.84
57.18
1.21
0
0.09
7470.1-1147-1216
CAGL0L09273g
4.84
24.29
0.95
0
0.09
6860.1-657-727
CAGL0J04004g
4.69
15.78
0.85
0
0.09
8147.1-1091-1160
CAGL0L04708g
4.51
16.92
0.91
0
0.08
2315.1-1226-1296
CAGL0J06402g
4.43
14.64
0.87
0
0.07
1207.1-1227-1297
CAGL0A03740g
4.43
12.24
0.82
0
0.07
2121.3-72-140
CAGL0I02134g
4.28
19.43
1
0
0.04
Total number of rows: 5908
Table truncated, full table size 300 Kbytes.
Table 4: The transcription profile of all genes in C. glabrata cells co-incubate with J774.1 murine macrophages for 6 hours (analyzed by SAM 2.0 software) header descriptions
Oligo ID
ID of each oligonucleotide used on microarray
ORF Name
Name of open reading frame corresponding to each oligonucleotide on the microarray
Score(d)
The T-statistic value calculated by SAM 2.0 software (The higher the absolute value of the Score, the more significant of a given transcript)
Macrophage/control (hr 6)
The average ratio of the level of a given transcript in yeast cells co-incubated with macrophages for 6 hrs versus in cells grown in medium alone for 6 hrs
Denominator(s+s0)
Denominator of the T-statistics
q-value(%)
The lowest false discovery rate of each given transcript
local fdr(%)
Local false discovery rate of each given transcript
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