Despite extensive studies, the fundamental mechanisms responsible for the development and progression of heart failure have not yet been fully elucidated. Recent experimental and clinical studies have suggested that reactive oxygen species (ROS) play a major pathological role. Quercetin, a major flavonoid present in the human diet, has been studied widely and its biological properties are consistent with its protective role in the cardiovascular system. However, it remains unknown whether the cardioprotective effects of quercetin may also occur through the modulation of genes involved in cell survival. This study was therefore designed to examine the gene expression profiling of cultured rat primary cardiomyocytes supplemented with quercetin using DNA-microarrays and relating these data to functional effects. Keywords: nutritional intervention, dose response
Overall design
Primary heart cell cultures were obtained by isolation of cardiomyocytes from the ventricles of 2–4 day old Wistar rats and grown until complete confluence. In some dishes, 30 μM quercetin was added to the culture medium for 6, 12 or 24 h. Total RNA was extracted using Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA), following the manufacturer’s protocol. The yield and purity of the RNA were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., Rockland, Del, USA). The 28s and 18s ribosomal bands were checked using Agilent 2100 bioanalyzer with an RNA 6000 Nano LabChip Kit. For each sample, mRNA was amplified starting from 1.5 μg of totRNA by Amino Allyl MessageAmp I aRNA Kit (Ambion Inc.) to obtain amino allyl antisense RNA (aaRNA). Labeling of aaRNA was performed using NHS ester Cy3 or Cy5 dies (Amersham Biosciences, Piscataway, NJ - USA). One hybridization to Agilent 22K-gene arrays (Rat oligo array G4130A) was performed to compare quercetin supplemented cells versus unsupplemented ones. Each analysis was replicated swapping the labeling with the two cyanine dyes.
Table 1: Quercetin treated cardiomyocytes for 6 hours (normalized data in which replicated expression profiles were combined to form ratio experiments where each gene is associated to a expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference) header descriptions
Sequence ID
Primary Sequence Name
Sequence Code
Sequence Name(s)
Sequence Description
Accession #
Log(Ratio)
Fold Change
P-value
Abs(Fold Change)
Log(Error)
Intensity1
Intensity2
Data table
Sequence ID
Primary Sequence Name
Sequence Code
Sequence Name(s)
Sequence Description
Accession #
Log(Ratio)
Fold Change
P-value
Abs(Fold Change)
Log(Error)
Intensity1
Intensity2
1129980
AI044448
AI044448
AI044448
Rattus norvegicus transcribed sequences
AI044448
0.04667
1.11344
0.28102
1.11344
0.04329
2766.1543
3100.35205
1129981
216732_Rn
AW435059
216732_Rn
similar to mouse hypothetical protein, clone MGC:18890 IMAGE:4239390, mRNA, complete cds.
216732_Rn
0.03536
1.08483
0.078
1.08483
0.02006
2640.95654
2865.82251
1129982
CB548214
CB548214
CB548214
Rattus norvegicus LOC363043 (LOC363043), mRNA
CB548214
-0.0158
-1.03706
0.83234
1.03706
0.07464
580.1778
548.3877
1129983
208332_Rn
AI176723
208332_Rn
similar to Mouse, FK506 binding protein 1a (12 kDa), clone MGC:6253 IMAGE:3498682, mRNA, complete cds.
Rattus norvegicus transcribed sequence with strong similarity to protein ref:NP_001978.1 (H.sapiens) ets variant gene 6; TEL1 oncogene [Homo sapiens]
BM384458
-0.02919
-1.06952
0.91192
1.06952
0.26388
101.81848
97.30073
1129987
207011_Rn
NM_053988
207011_Rn
Rattus norvegicus calbindin 2 (Calb2), mRNA.
207011_Rn
-0.07439
-1.18685
0.21977
1.18685
0.06062
601.1239
503.28223
1129988
AI111924
AI111924
AI111924
Rattus norvegicus transcribed sequences
AI111924
-0.04338
-1.10504
0.74063
1.10504
0.13105
286.98431
252.608
1129989
BQ201015
BQ201015
BQ201015
Rattus norvegicus transcribed sequence with strong similarity to protein ref:NP_005157.1 (H.sapiens) amyloid beta (A4) precursor-like protein 1 [Homo sapiens]
BQ201015
-0.05284
-1.12937
0.06295
1.12937
0.02841
5566.95312
4901.60156
1129990
AW533710
AW533710
AW533710
Rattus norvegicus transcribed sequences
AW533710
0.00931
1.02166
0.95254
1.02166
0.15638
1109.85474
1132.76697
1129991
CA511303
CA511303
CA511303
Rattus norvegicus similar to hypothetical protein (LOC307138), mRNA
CA511303
0.04892
1.11922
0.41679
1.11922
0.06024
526.58289
586.25854
1129992
CB546125
CB546125
CB546125
Rattus norvegicus similar to Als2 (LOC363235), mRNA
CB546125
-0.05188
-1.12688
0.64578
1.12688
0.11286
274.37238
241.5106
1129993
232354_Rn
BF396356
232354_Rn
similar to Mouse Strain C57BL6/J chromosome 19 BAC, RP22-325J22, Complete Sequence, complete sequence.
similar to Mouse glutaryl-CoA dehydrogenase mRNA, complete cds.
216438_Rn
-0.00735
-1.01708
0.71443
1.01708
0.0201
4355.17529
4287.49365
1129997
CB547916
CB547916
CB547916
Rattus norvegicus similar to cullin 4B; Cullin-4B (LOC302502), mRNA
CB547916
-0.12078
-1.32064
0.06532
1.32064
0.06553
612.47607
459.92194
1129998
Sca1
NM_012726
Sca1
spinocerebellar ataxia 1 homolog (human)
NM_012726
-0.007
-1.01626
0.98497
1.01626
0.37183
94.60399
75.93189
1129999
Gnao
NM_017327
Gnao
guanine nucleotide binding protein, alpha o
NM_017327
0.36032
2.29255
2.65E-06
2.29255
0.07673
2225.17505
5322.59082
Total number of rows: 20280
Table truncated, full table size 3657 Kbytes.
Table 2: Quercetin treated cardiomyocytes for 12 hours (normalized data in which replicated expression profiles were combined to form ratio experiments where each gene is associated to a expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference) header descriptions
Sequence ID
Primary Sequence Name
Sequence Code
Sequence Name(s)
Sequence Description
Accession #
Log(Ratio)
Fold Change
P-value
Abs(Fold Change)
Log(Error)
Intensity1
Intensity2
Data table
Sequence ID
Primary Sequence Name
Sequence Code
Sequence Name(s)
Sequence Description
Accession #
Log(Ratio)
Fold Change
P-value
Abs(Fold Change)
Log(Error)
Intensity1
Intensity2
1129980
AI044448
AI044448
AI044448
Rattus norvegicus transcribed sequences
AI044448
-0.02661
-1.0632
0.40968
1.0632
0.03228
3293.60986
3099.27197
1129981
216732_Rn
AW435059
216732_Rn
similar to mouse hypothetical protein, clone MGC:18890 IMAGE:4239390, mRNA, complete cds.
216732_Rn
0.01015
1.02365
0.68828
1.02365
0.0253
3250.87744
3325.68457
1129982
CB548214
CB548214
CB548214
Rattus norvegicus LOC363043 (LOC363043), mRNA
CB548214
0.01425
1.03335
0.74814
1.03335
0.04437
953.07764
992.12201
1129983
208332_Rn
AI176723
208332_Rn
similar to Mouse, FK506 binding protein 1a (12 kDa), clone MGC:6253 IMAGE:3498682, mRNA, complete cds.
Rattus norvegicus transcribed sequence with strong similarity to protein ref:NP_001978.1 (H.sapiens) ets variant gene 6; TEL1 oncogene [Homo sapiens]
BM384458
0.00659
1.01528
0.9875
1.01528
0.42024
84.00959
96.07262
1129987
207011_Rn
NM_053988
207011_Rn
Rattus norvegicus calbindin 2 (Calb2), mRNA.
207011_Rn
-0.00954
-1.0222
0.84272
1.0222
0.04807
856.13538
844.36975
1129988
AI111924
AI111924
AI111924
Rattus norvegicus transcribed sequences
AI111924
-0.00546
-1.01266
0.96433
1.01266
0.12218
374.14514
386.3696
1129989
BQ201015
BQ201015
BQ201015
Rattus norvegicus transcribed sequence with strong similarity to protein ref:NP_005157.1 (H.sapiens) amyloid beta (A4) precursor-like protein 1 [Homo sapiens]
BQ201015
-0.02322
-1.05491
0.47837
1.05491
0.03275
7030.41943
6660.79346
1129990
AW533710
AW533710
AW533710
Rattus norvegicus transcribed sequences
AW533710
-0.08401
-1.21341
0.58839
1.21341
0.15523
1474.07764
1255.5376
1129991
CA511303
CA511303
CA511303
Rattus norvegicus similar to hypothetical protein (LOC307138), mRNA
CA511303
-0.02999
-1.07148
0.59837
1.07148
0.05693
595.90027
559.84778
1129992
CB546125
CB546125
CB546125
Rattus norvegicus similar to Als2 (LOC363235), mRNA
CB546125
0.0116
1.02707
0.88916
1.02707
0.08324
354.5871
367.1814
1129993
232354_Rn
BF396356
232354_Rn
similar to Mouse Strain C57BL6/J chromosome 19 BAC, RP22-325J22, Complete Sequence, complete sequence.
similar to Mouse glutaryl-CoA dehydrogenase mRNA, complete cds.
216438_Rn
0.09558
1.24617
6.12E-06
1.24617
0.02113
5770.99512
7183.61328
1129997
CB547916
CB547916
CB547916
Rattus norvegicus similar to cullin 4B; Cullin-4B (LOC302502), mRNA
CB547916
-0.02294
-1.05425
0.68975
1.05425
0.05748
743.89478
713.3501
1129998
Sca1
NM_012726
Sca1
spinocerebellar ataxia 1 homolog (human)
NM_012726
-0.07191
-1.18007
0.77431
1.18007
0.25077
186.08755
159.67957
1129999
Gnao
NM_017327
Gnao
guanine nucleotide binding protein, alpha o
NM_017327
0.07963
1.20123
0.26975
1.20123
0.07215
2538.23389
3120.27686
Total number of rows: 20280
Table truncated, full table size 3653 Kbytes.
Table 3: Quercetin treated cardiomyocytes for 24 hours (normalized data in which replicated expression profiles were combined to form ratio experiments where each gene is associated to a expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference) header descriptions
Sequence ID
Primary Sequence Name
Sequence Code
Sequence Name(s)
Sequence Description
Accession #
Log(Ratio)
Fold Change
P-value
Abs(Fold Change)
Log(Error)
Intensity1
Intensity2
Data table
Sequence ID
Primary Sequence Name
Sequence Code
Sequence Name(s)
Sequence Description
Accession #
Log(Ratio)
Fold Change
P-value
Abs(Fold Change)
Log(Error)
Intensity1
Intensity2
1129980
AI044448
AI044448
AI044448
Rattus norvegicus transcribed sequences
AI044448
-0.0394
-1.09497
0.30656
1.09497
0.03854
2933.51953
2670.11914
1129981
216732_Rn
AW435059
216732_Rn
similar to mouse hypothetical protein, clone MGC:18890 IMAGE:4239390, mRNA, complete cds.
216732_Rn
0.03952
1.09528
0.0663
1.09528
0.02152
2869.38403
3143.46436
1129982
CB548214
CB548214
CB548214
Rattus norvegicus LOC363043 (LOC363043), mRNA
CB548214
0.00406
1.0094
0.90678
1.0094
0.03468
995.81836
1001.7135
1129983
208332_Rn
AI176723
208332_Rn
similar to Mouse, FK506 binding protein 1a (12 kDa), clone MGC:6253 IMAGE:3498682, mRNA, complete cds.
Rattus norvegicus transcribed sequence with strong similarity to protein ref:NP_001978.1 (H.sapiens) ets variant gene 6; TEL1 oncogene [Homo sapiens]
BM384458
0.1029
1.26735
0.71129
1.26735
0.27801
81.47382
98.2209
1129987
207011_Rn
NM_053988
207011_Rn
Rattus norvegicus calbindin 2 (Calb2), mRNA.
207011_Rn
-0.0311
-1.07424
0.43831
1.07424
0.04013
886.59497
819.33337
1129988
AI111924
AI111924
AI111924
Rattus norvegicus transcribed sequences
AI111924
0.04635
1.11264
0.57919
1.11264
0.08358
379.37598
402.34106
1129989
BQ201015
BQ201015
BQ201015
Rattus norvegicus transcribed sequence with strong similarity to protein ref:NP_005157.1 (H.sapiens) amyloid beta (A4) precursor-like protein 1 [Homo sapiens]
BQ201015
0.01692
1.03972
0.60186
1.03972
0.03242
6259.42773
6533.54639
1129990
AW533710
AW533710
AW533710
Rattus norvegicus transcribed sequences
AW533710
0.01439
1.03368
0.93696
1.03368
0.1819
1309.06531
1270.2428
1129991
CA511303
CA511303
CA511303
Rattus norvegicus similar to hypothetical protein (LOC307138), mRNA
CA511303
0.08563
1.21794
0.04237
1.21794
0.04218
552.17542
668.02527
1129992
CB546125
CB546125
CB546125
Rattus norvegicus similar to Als2 (LOC363235), mRNA
CB546125
0.00722
1.01676
0.9365
1.01676
0.09058
348.12274
336.5271
1129993
232354_Rn
BF396356
232354_Rn
similar to Mouse Strain C57BL6/J chromosome 19 BAC, RP22-325J22, Complete Sequence, complete sequence.