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Status
Public on Jan 03, 2008
Title
Methyl mercury 24h
Sample type
RNA
Channel 1
Source name
mRNA from zebrafish embryos that were exposed to Methyl mercury 24h
Organism
Danio rerio
Characteristics
whole body mRNA Strains: 200-800 zebrafish from AB*,AB2O2,AB2O2 Golden and AB2O2 Leo whole body mRNA Strains: 200-800 zebrafish from AB*,AB2O2,AB2O2 Golden and AB2O2 Leo
Biomaterial provider
Fish Facility at the Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe
Treatment protocol
Acrylamide (CH2=CHCONH2), Aroclor 1254 (PCB), Arsenic(III) Oxide (As2O3), tBHQ (tert-Butylhydroquinone (CH3)3CC6H3-1,4-(OH)2), Cadmiumchloride (CdCl2.2H2O), 4-Chloroaniline (ClC6H4NH2), DDT (1,1-Bis-(4-Chlorphenyl)-2,2,2-Trichlorethan (ClC6H4)2CHCCl3), Lead (II)chloride (PbCl2), Methylmercurychloride (CH3ClHg), TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) and Valproic acid (CH3(CH2)4CO2H) were purchased from Sigma-Aldrich. Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. Embryos were grown in embryo medium (60 ug/ml Instant Ocean, Red Sea Fish Pharm Ltd.) Different numbers of embryos were exposed to the chemicals: between 4 to 24 hpf (600 embryos), 24 to 48 hpf (400 embryos) and 96 to 120 hpf (200 embryos). Embryo medium alone (Cd, Hg, Pb, As, VA, AA) or 0.2 % ethanol in embryo medium (tBHQ , 4CA, PCB, DDT) or 0.5% DMSO, 28mg/l toluene in embryo medium (TCDD) were used as vehicle controls. The toxin concentrations were adjusted in such a way that embryo death was minimal. The few dead embryos were discarded before preparation of RNA.
Growth protocol
as described in Westerfield 1993
Extracted molecule
polyA RNA
Extraction protocol
1) Total RNA was isolated using the Nucleospin RNA L Kit (Macherey-Nagel, Dueren, Germany). 2) mRNA was extracted with the Ambion Purist Kit (Austin, TX).
Label
Cy5
Label protocol
Labeled cDNA was synthesized from 1-2 ug mRNA using the Amersham direct cDNA labeling kit (Amersham Europe, Freiburg, Germany).
Channel 2
Source name
mRNA from zebrafish embryos that were not exposed to a toxic environment
Organism
Danio rerio
Characteristics
Strains: 200-800 zebrafish from AB*,AB2O2,AB2O2 Golden and AB2O2 Leo whole body mRNA
Biomaterial provider
Fish Facility at the Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe
Treatment protocol
Acrylamide (CH2=CHCONH2), Aroclor 1254 (PCB), Arsenic(III) Oxide (As2O3), tBHQ (tert-Butylhydroquinone (CH3)3CC6H3-1,4-(OH)2), Cadmiumchloride (CdCl2.2H2O), 4-Chloroaniline (ClC6H4NH2), DDT (1,1-Bis-(4-Chlorphenyl)-2,2,2-Trichlorethan (ClC6H4)2CHCCl3), Lead (II)chloride (PbCl2), Methylmercurychloride (CH3ClHg), TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) and Valproic acid (CH3(CH2)4CO2H) were purchased from Sigma-Aldrich. Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. Embryos were grown in embryo medium (60 ug/ml Instant Ocean, Red Sea Fish Pharm Ltd.) Different numbers of embryos were exposed to the chemicals: between 4 to 24 hpf (600 embryos), 24 to 48 hpf (400 embryos) and 96 to 120 hpf (200 embryos). Embryo medium alone (Cd, Hg, Pb, As, VA, AA) or 0.2 % ethanol in embryo medium (tBHQ , 4CA, PCB, DDT) or 0.5% DMSO, 28mg/l toluene in embryo medium (TCDD) were used as vehicle controls. The toxin concentrations were adjusted in such a way that embryo death was minimal. The few dead embryos were discarded before preparation of RNA.
Growth protocol
as described in Westerfield 1993
Extracted molecule
polyA RNA
Extraction protocol
1) Total RNA was isolated using the Nucleospin RNA L Kit (Macherey-Nagel, Dueren, Germany). 2) mRNA was extracted with the Ambion Purist Kit (Austin, TX).
Label
Cy3
Label protocol
Labeled cDNA was synthesized from 1-2 ug mRNA using the Amersham direct cDNA labeling kit (Amersham Europe, Freiburg, Germany).
Hybridization protocol
1) Removal of unincorporated nucleotides over Microcon 30 spin columns (Millipore, Bedford, MA). 2) The concentrated probes were hybridized to the microarray in 1xDIG Easy-Hyb buffer (Hoffmann-La Roche, Basel, CH) overnight at 42 C. 3) Cover slips were removed from the slides by flushing with 4xSSC. 4) Slides were washed in pre-warmed wash buffer 1 (2xSSC, 0.1% SDS) for 5 minutes at 42 C. 5) Washing in buffer 2 (0.1xSSC, 0.1% SDS) for 10 minutes at room temperature. 6) Washing in 0.1xSSC four times for 1 min at room temperature. 7) The slides were briefly dipped into 0.01xSSC at room temperature. 8) Centrifugation for 7 min at 800 rpm in an Eppendorf 5810R centrifuge.
Scan protocol
1) Scanned on an GenePix 4000B dual-laser scanner from Molecular Devices 2) Both channels (532 nm for Cy3 and 635 nm for Cy5) were scanned in parallel 3) Data was stored as 16-bit TIFF files 4) The channels for Cy3 and Cy5 were balanced in each scan for approximately the same intensity profile. 5) Each array was scanned three times (low, medium and high scan) with different signal amplification factors (voltage settings of the photomultiplier tubes), but with the same laser power. 6) Raw data was retrieved with GenePix Pro 6.0 software from Axon Instruments . 7) Data processing was performed 8) The absolute intensity values span the range from 0 to 65536. 9) The scans were performed with a resolution of 10 um.
Description
This file contains all technological and biological replicates (i.e. from the same and different biological source, repspectively) that were performed with this particular toxin at this particular concentration. The Dye-Swap Designe was utilised.
Data processing
1) Raw data are retrieved with GenePix 2) Quality control on spot level 3) Local background correction. 4) Averaging of the two spots for each gene. 5) Consensus signals are calculated from low, medium and high scan based on a Least Squares Algorithm. 6) Log transformation. 7) locally weighted regression smoother (LOESS). 8) Scaling to a common MAD. 9) t-test 10) adjustment of p-values for multiplicity 11) Quality control on array level.
Submission date
Aug 29, 2007
Last update date
Jan 02, 2008
Contact name
Jessica Legradi
Organization name
Karlsruhe Institute of Technology
Department
Institute of Toxicology and Genomics ITG
Lab
Straehle
Street address
Hermann-von-Helmholtz-Platz 1
City
Eggenstein-Leopoldshafen
State/province
Baden-Wuerttemberg
ZIP/Postal code
76344
Country
Germany
Platform ID
GPL4603
Series (1)
Data table header descriptions
ID_REF
spot/gene id (numbered from 1-34992)
VALUE
normalized log naturalis ratios (M or M.bar value) (test/reference)
res_A.bar
averaged log naturalis average
res_M.var
variance of VALUE
res_M.se
standard error of VALUE
res_par.state1
Check for reliability of p-value and fold change: A.bar + 0.5 * M.bar
res_par.state2
Check for reliability of p-value and fold change: A.bar - 0.5 * M.bar
res_t
test statistic of t-test for this gene
res_t.reg
test statistic of regularized t-test for this gene
res_fc
fold change
res_p.value
p-value for t-test
res_p.adj
adjusted p-value for t-test
res_wilcox.stat
test statistic for wilcoxon test
res_p.value.adj.wil
adjusted p-value for wilcoxon test
res_good.arrays
numnber of good flags (after quality control) for this gene
res_comment1
Comment if FC is not reliable
res_comment2
Comment if t and regularized t-values are not reliable
NA.
norm_flag_Array1
flag if spot is good (1) or bad (0)
norm_flag_Array2
norm_flag_Array3
norm_flag_Array4
norm_flag_Array5
norm_flag_Array6
norm_flag_Array7
norm_flag_Array8
norm_R_Array1
Red signal after normalization
norm_R_Array2
norm_R_Array3
norm_R_Array4
norm_R_Array5
norm_R_Array6
norm_R_Array7
norm_R_Array8
norm_G_Array1
Green signal after normalization
norm_G_Array2
norm_G_Array3
norm_G_Array4
norm_G_Array5
norm_G_Array6
norm_G_Array7
norm_G_Array8
norm_M_Array1
M value after normalization
norm_M_Array2
norm_M_Array3
norm_M_Array4
norm_M_Array5
norm_M_Array6
norm_M_Array7
norm_M_Array8
norm_A_Array1
A value after normalization
norm_A_Array2
norm_A_Array3
norm_A_Array4
norm_A_Array5
norm_A_Array6
norm_A_Array7
norm_A_Array8
norm_C_Array1
Normalization constant that will be added to signal
norm_C_Array2
norm_C_Array3
norm_C_Array4
norm_C_Array5
norm_C_Array6
norm_C_Array7
norm_C_Array8
avg_R_Array1
Red channel value after averaging of scans
avg_R_Array2
avg_R_Array3
avg_R_Array4
avg_R_Array5
avg_R_Array6
avg_R_Array7
avg_R_Array8
avg_G_Array1
Green channel value after averaging of scans
avg_G_Array2
avg_G_Array3
avg_G_Array4
avg_G_Array5
avg_G_Array6
avg_G_Array7
avg_G_Array8
avg_flag_Array1
Flag (good/bad spot) value after averaging of scans
avg_flag_Array2
avg_flag_Array3
avg_flag_Array4
avg_flag_Array5
avg_flag_Array6
avg_flag_Array7
avg_flag_Array8
Data table
ID_REF
VALUE
res_A.bar
res_M.var
res_M.se
res_par.state1
res_par.state2
res_t
res_t.reg
res_fc
res_p.value
res_p.adj
res_wilcox.stat
res_p.value.adj.wil
res_good.arrays
res_comment1
res_comment2
NA.
norm_flag_Array1
norm_flag_Array2
norm_flag_Array3
norm_flag_Array4
norm_flag_Array5
norm_flag_Array6
norm_flag_Array7
norm_flag_Array8
norm_R_Array1
norm_R_Array2
norm_R_Array3
norm_R_Array4
norm_R_Array5
norm_R_Array6
norm_R_Array7
norm_R_Array8
norm_G_Array1
norm_G_Array2
norm_G_Array3
norm_G_Array4
norm_G_Array5
norm_G_Array6
norm_G_Array7
norm_G_Array8
norm_M_Array1
norm_M_Array2
norm_M_Array3
norm_M_Array4
norm_M_Array5
norm_M_Array6
norm_M_Array7
norm_M_Array8
norm_A_Array1
norm_A_Array2
norm_A_Array3
norm_A_Array4
norm_A_Array5
norm_A_Array6
norm_A_Array7
norm_A_Array8
norm_C_Array1
norm_C_Array2
norm_C_Array3
norm_C_Array4
norm_C_Array5
norm_C_Array6
norm_C_Array7
norm_C_Array8
avg_R_Array1
avg_R_Array2
avg_R_Array3
avg_R_Array4
avg_R_Array5
avg_R_Array6
avg_R_Array7
avg_R_Array8
avg_G_Array1
avg_G_Array2
avg_G_Array3
avg_G_Array4
avg_G_Array5
avg_G_Array6
avg_G_Array7
avg_G_Array8
avg_flag_Array1
avg_flag_Array2
avg_flag_Array3
avg_flag_Array4
avg_flag_Array5
avg_flag_Array6
avg_flag_Array7
avg_flag_Array8
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t and regul. t values unreliable
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t and regul. t values unreliable
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TRUE
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t and regul. t values unreliable
FALSE
TRUE
TRUE
TRUE
TRUE
FALSE
TRUE
TRUE
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24
0.595874279592138
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10.1190144375302
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TRUE
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11
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5.80452581637762
0.31044749610877
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0.793881434683816
1.20915071229066
0.51049479010016
0.621416325582161
4
0.848606350643472
3
t and regul. t values unreliable
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
FALSE
12
0.179353455726828
7.84318770088756
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0.137351557516972
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27
0.356653620352251
8
TRUE
TRUE
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TRUE
TRUE
TRUE
TRUE
8.76986413876964
8.23289887672672
7.55379955390681
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6.780732518646
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TRUE
TRUE
TRUE
TRUE
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TRUE
TRUE
TRUE
13
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11.5806357994269
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34
0.0455523772495001
8
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
12.4888746112778
11.7047186318000
11.1606787423012
11.3990364663929
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11.5632284363464
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TRUE
TRUE
TRUE
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14
0.077879587645386
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0.00215876516573507
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1.90174402195426
1.08099248598248
0.0989519098103435
0.166291673618458
36
0.0162994872406392
8
t and regul. t values unreliable
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
9.3594701640094
9.04319809037942
8.28756299935664
8.16052365124123
8.63788887512194
8.40418617020552
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4179.84911036292
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6604.81857105185
6830.050083371
2741.31958455223
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TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
15
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0.022072468712801
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-1.05218800567294
0.473537527032325
0.587256349089705
11
0.509950319780722
8
t and regul. t values unreliable
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
8.1430644869551
7.51406438892837
6.94807573448065
7.59087089975314
7.81968745157161
7.31850442106795
6.83507600583718
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3158.50120442563
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TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
16
0.0346935449939437
9.24493628955523
0.0353509451154989
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21
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8
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
9.99882957113147
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9470.60593967125
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13606.7271612792
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TRUE
TRUE
TRUE
TRUE
TRUE
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TRUE
TRUE
17
0.05078787664291
7.0729464223416
0.0139669880126783
0.0684185265317669
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0.742311757025768
1.05209969469199
0.482058641712257
0.594536726025494
28
0.293471959807626
8
t and regul. t values unreliable
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
8.08314635523804
7.23384284369755
6.53157077111804
7.140425770256
7.41761964566743
7.08176250926922
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1017.50766909717
352
625.207345027315
3440.93771176901
1929.56260936008
977.982557305852
1529.72197091971
2020.37246482067
1531.63228252733
558
745.685626155895
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
18
0.0770602339160235
8.01568285526776
0.00782315787146306
0.0502401863844554
8.05421297222577
7.97715273830975
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1.53383654523755
1.08010713351563
0.168939391704339
0.263015091409424
32
0.0970299665348342
8
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
9.0386079800389
8.39990932201426
7.69185958823616
7.70693525881176
8.35168463479916
7.85214622592173
6.95013417831245
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2180.38520121710
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1782.68365492283
11173.9789840430
5391.74199827125
2083.63091769216
3071.30327314112
4753.02733475041
3919.25830379143
1508.00730242794
2116.99389865754
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
19
0.0163976632943579
6.09784027281522
0.000393608671795734
0.178032794239473
6.1060391044624
6.08964144116804
1.16886575033761
0.0921047347731972
1.01653284284059
0.941529273555025
0.960524558024415
3
0.620909929732415
2
FC is not reliable
t and regul. t values unreliable
t and regul. t values unreliable
FALSE
TRUE
FALSE
FALSE
TRUE
FALSE
FALSE
FALSE
6.25244630457043
5.60925626325679
6.25765655141256
5.69085701677356
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407
205.753758268110
666
392.852087936716
FALSE
TRUE
FALSE
FALSE
TRUE
FALSE
FALSE
FALSE
20
0.051695388014907
9.14482533355923
0.0202094438147331
0.0580170342800043
9.17067302756669
9.11897763955178
1.02853627247138
0.891038100386388
1.05305492050298
0.402495085890073
0.520509997268376
25
0.509950319780722
8
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
10.0581548245993
9.44700946241496
8.63923846571882
8.6997173386932
9.38821500948278
8.98082902068233
8.24609232588737
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Total number of rows: 34992 Table truncated, full table size 24178 Kbytes .Supplementary data files not provided
Processed data included within Sample table