^SAMPLE = Control Embyronic Stem Cell Replicate 1
!Sample_title = Control Embyronic Stem Cell Replicate 1
!Sample_supplementary_file = file1.gpr
!Sample_source_name_ch1 = Total RNA from murine ES-D3 embryonic stem cells labeled with Cyanine-5 (red).
!Sample_organism_ch1 = Mus musculus
!Sample_characteristics_ch1 = ES-D3 cell line (CRL-1934)
!Sample_characteristics_ch1 = Age: day 4 
!Sample_characteristics_ch1 = Tissue: blastocytes
!Sample_characteristics_ch1 = Strain: 129/Sv mice
!Sample_growth_protocol_ch1 = ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cultured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modified Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoethanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.
!Sample_extract_protocol_ch1 = TriZol procedure
!Sample_molecule_ch1 = total RNA
!Sample_label_ch1 = Cy5
!Sample_label_protocol_ch1 = 10 g of total RNA were primed with 2 l of 100 M T16N2 DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M each dATP, dTTP, dGTP, with 25 M dCTP, 25 M Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).
!Sample_source_name_ch2 = Total RNA from pooled whole mouse embryos e17.5, labeled with Cyanine-3 (green).
!Sample_organism_ch2 = Mus musculus
!Sample_characteristics_ch2 = Strain: C57BL/6
!Sample_characteristics_ch2 = Age: e17.5 d
!Sample_characteristics_ch2 = Tissue: whole embryo
!Sample_extract_protocol_ch2 = TriZol procedure
!Sample_molecule_ch2 = total RNA
!Sample_label_ch2 = Cy3
!Sample_label_protocol_ch2 = 10 g of total RNA were primed with 2 l of 100 M T16N2 DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M each dATP, dTTP, dGTP, with 25 M dCTP, 25 M Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).
!Sample_hyb_protocol = Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 17 h at 60C in a rotating oven, and washed.
!Sample_scan_protocol = Scanned on an Agilent G2565AA scanner.
!Sample_scan_protocol = Images were quantified using Agilent Feature Extraction Software (version A.7.5). 
!Sample_description = Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.
!Sample_data_processing = LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.
!Sample_platform_id = GPL3759
#ID_REF = 
#VALUE = log(REDsignal/GREENsignal) per feature (processed signals used).
#LogRatioError = error of the log ratio calculated according to the error model chosen.
#PValueLogRatio = Significance level of the Log Ratio computed for a feature.
#gProcessedSignal = Dye-normalized signal after surrogate "algorithm," green "channel," used for computation of log ratio.
#rProcessedSignal = Dye-normalized signal after surrogate "algorithm," red "channel," used for computation of log ratio.
!sample_table_begin	
ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal
1	-1.6274758	1.36E-01	6.41E-33	9.13E+03	2.15E+02
2	0.1412248	1.34E+00	1.00E+00	4.14E+01	5.72E+01
3	0.1827684	5.19E-02	4.33E-04	5.13E+03	7.81E+03
4	-0.3932267	6.08E-02	1.02E-10	4.65E+03	1.88E+03
5	-0.9865994	1.05E-01	6.32E-21	2.91E+03	3.01E+02
6	0.0238812	1.02E-01	8.15E-01	7.08E+02	7.48E+02
7	-1.4841822	1.25E-01	1.42E-32	1.02E+04	3.36E+02
8	-1.8261356	4.15E-01	1.10E-05	7.19E+02	1.07E+01
9	-1.0344779	1.78E+00	1.00E+00	9.62E+01	8.89E+00
10	0.2405891	3.09E-01	4.36E-01	1.61E+02	2.80E+02
11	0.3209366	3.59E-01	3.71E-01	1.25E+02	2.61E+02
12	0.358304	2.06E+00	1.00E+00	2.04E+01	4.66E+01
13	-0.0122072	3.64E-01	9.73E-01	1.84E+02	1.79E+02
14	-1.5480396	1.30E-01	7.21E-33	1.02E+04	2.90E+02
15	0.0073419	2.98E-01	9.80E-01	2.21E+02	2.25E+02
16	-0.2267015	9.44E-01	8.10E-01	8.90E+01	5.28E+01
17	-0.1484023	8.01E-01	8.53E-01	9.65E+01	6.86E+01
18	-0.6122195	1.28E-01	1.69E-06	1.12E+03	2.73E+02
19	0.0796905	8.78E-02	3.64E-01	8.21E+02	9.87E+02
20	-0.084895	9.38E-01	9.28E-01	7.68E+01	6.32E+01
!sample_table_end	
^SAMPLE = Control Embyronic Stem Cell Replicate 2	
!Sample_title = Control Embyronic Stem Cell Replicate 2
!Sample_supplementary_file = file2.gpr	
!Sample_source_name_ch1 = Total RNA from murine ES-D3 embryonic stem cells labeled with Cyanine-5 (red).	
!Sample_organism_ch1 = Mus musculus	
!Sample_characteristics_ch1 = ES-D3 cell line (CRL-1934)	
!Sample_characteristics_ch1 = Age: day 4 	
!Sample_characteristics_ch1 = Tissue: blastocytes	
!Sample_characteristics_ch1 = Strain: 129/Sv mice	
!Sample_growth_protocol_ch1 = ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cultured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modified Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoethanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.
!Sample_extract_protocol_ch1 = TriZol procedure	
!Sample_molecule_ch1 = total RNA	
!Sample_label_ch1 = Cy5	
!Sample_label_protocol_ch1 = 10 g of total RNA were primed with 2 l of 100 M T16N2 DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M each dATP, dTTP, dGTP, with 25 M dCTP, 25 M Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).
!Sample_source_name_ch2 = Total RNA from pooled whole mouse embryos e17.5, labeled with Cyanine-3 (green).	
!Sample_organism_ch2 = Mus musculus	
!Sample_characteristics_ch2 = Strain: C57BL/6	
!Sample_characteristics_ch2 = Age: e17.5 d	
!Sample_characteristics_ch2 = Tissue: whole embryo	
!Sample_extract_protocol_ch2 = TriZol procedure	
!Sample_molecule_ch2 = total RNA	
!Sample_label_ch2 = Cy3
!Sample_label_protocol_ch2 = 10 g of total RNA were primed with 2 l of 100 M T16N2 DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M each dATP, dTTP, dGTP, with 25 M dCTP, 25 M Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).
!Sample_hyb_protocol = Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 17 h at 60C in a rotating oven, and washed.
!Sample_scan_protocol = Scanned on an Agilent G2565AA scanner.	
!Sample_scan_protocol = Images were quantified using Agilent Feature Extraction Software (version A.7.5). 	
!Sample_description = Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.	
!Sample_data_processing = LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.	
!Sample_platform_id = GPL3759
#ID_REF = 	
#VALUE = log(REDsignal/GREENsignal) per feature (processed signals used).	
#LogRatioError = error of the log ratio calculated according to the error model chosen.	
#PValueLogRatio = Significance level of the Log Ratio computed for a feature.	
#gProcessedSignal = Dye-normalized signal after surrogate "algorithm," green "channel," used for computation of log ratio.	
#rProcessedSignal = Dye-normalized signal after surrogate "algorithm," red "channel," used for computation of log ratio.	
!sample_table_begin	
ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal
1	-1.1697263	1.23E-01	2.14E-21	3.17E+03	2.14E+02
2	-0.1111353	1.63E+00	9.46E-01	5.43E+01	4.20E+01
3	0.1400597	5.11E-02	6.17E-03	6.72E+03	9.28E+03
4	-0.4820633	6.38E-02	4.06E-14	6.46E+03	2.13E+03
5	-1.2116196	1.22E-01	2.31E-23	3.62E+03	2.22E+02
6	-0.0230528	1.04E-01	8.24E-01	8.76E+02	8.31E+02
7	-1.1380152	1.13E-01	9.23E-24	3.94E+03	2.86E+02
8	-1.834596	5.40E-01	6.74E-04	6.44E+02	9.43E+00
9	-0.9747637	2.14E+00	1.00E+00	9.17E+01	9.72E+00
10	0.3874005	2.92E-01	1.85E-01	1.69E+02	4.11E+02
11	0.5340442	3.29E-01	1.04E-01	1.23E+02	4.20E+02
12	0.3260696	1.92E+00	8.65E-01	2.73E+01	5.77E+01
13	0.3010618	2.84E-01	2.90E-01	1.93E+02	3.87E+02
14	-1.0760413	1.08E-01	1.63E-23	4.06E+03	3.41E+02
15	-0.1167371	3.87E-01	7.63E-01	2.32E+02	1.77E+02
16	-0.1936322	9.44E-01	8.38E-01	1.02E+02	6.56E+01
17	-0.3275898	7.87E-01	6.77E-01	1.41E+02	6.65E+01
18	-0.4805853	1.14E-01	2.41E-05	1.34E+03	4.42E+02
19	0.1109524	9.56E-02	2.46E-01	8.38E+02	1.08E+03
20	0.1677912	6.51E-01	7.97E-01	9.84E+01	1.45E+02
!sample_table_end	
^SAMPLE = Triple-Fusion Transfected Embryonic Stem Cells Replicate 1
!Sample_supplementary_file = file3.gpr	
!Sample_title = Triple-Fusion Transfected Embryonic Stem Cells Replicate 1	
!Sample_source_name_ch1 = Total RNA from murine ES-D3 triple-transfected embryonic stem cells labeled with Cyanine-5 (red).	
!Sample_organism_ch1 = Mus musculus	
!Sample_characteristics_ch1 = ES-D3 cell line (CRL-1934)	
!Sample_characteristics_ch1 = Transfected with pUb-fluc-mrfp-ttk triple fusion reporter gene.	
!Sample_characteristics_ch1 = Age: day 4 	
!Sample_characteristics_ch1 = Tissue: blastocytes	
!Sample_characteristics_ch1 = Strain: 129/Sv mice	
!Sample_treatment_protocol_ch1 = PCR amplification and standard cloning techniques were used to insert fluc and mrfp genes from plasmids pCDNA 3.1-CMV-fluc (Promega, Madison, WI) and pCDNA3.1-CMV-mrfp in frame with the ttk gene into the pCDNA3.1-truncated	sr39tk. This triple fusion (TF) reporter gene fragment (3.3 kbp) was released from the plasmid with Not1 and BamH1 restriction enzymes before blunt-end ligation into the multiple cloning site of lentiviral transfer vector, FUG, driven by the human ubiquitin-C promoter. Self-inactivating (SIN) lentivirus was prepared by transient transfection of 293T cells. Briefly, pFUG-TF containing the triple fusion reporter gene was co-transfected into 293T cells with HIV-1 packaging vector (?8.9) and vesicular stomatitis virus G glycoprotein-pseudotyped envelop vector (pVSVG). Lentivirus supernatant was concentrated by sediment centrifugation using a SW29 rotor at 50,000 x g for two hours. Concentrated virus was titered on 293T cells. Murine ES cells were transfected with LV-pUb-fluc-mrfp-ttk at a multiplicity of infection (MOI) of 10.
!Sample_growth_protocol_ch1 = ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cultured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modified Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoethanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.
!Sample_extract_protocol_ch1 = TriZol procedure	
!Sample_molecule_ch1 = total RNA	
!Sample_label_ch1 = Cy5	
!Sample_label_protocol_ch1 = 10 g of total RNA were primed with 2 l of 100 M T16N2 DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M each dATP, dTTP, dGTP with 25 M dCTP, 25 M Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).	
!Sample_source_name_ch2 = Total RNA from pooled whole mouse embryos e17.5, labeled with Cyanine-3 (green).	
!Sample_organism_ch2 = Mus musculus	
!Sample_characteristics_ch2 = Strain: C57BL/6	
!Sample_characteristics_ch2 = Age: e17.5 d	
!Sample_characteristics_ch2 = Tissue: whole embryo	
!Sample_extract_protocol_ch2 = TriZol procedure	
!Sample_molecule_ch2 = total RNA	
!Sample_label_ch2 = Cy3	
!Sample_label_protocol_ch2 = 10 g of total RNA were primed with 2 l of 100 M T16N2 DNA primer at 70C for 10 min, then reversed transcribed at 42C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M each dATP, dTTP, dGTP, with 25 M dCTP, 25 M Cy5-labeled dCTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).
!Sample_hyb_protocol = Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 17 h at 60C in a rotating oven, and washed.
!Sample_scan_protocol = Scanned on an Agilent G2565AA scanner.	
!Sample_description = Biological replicate 1 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.	
!Sample_data_processing = LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.	
!Sample_platform_id = GPL3759
#ID_REF = 	
#VALUE = log(REDsignal/GREENsignal) per feature (processed signals used).	
#LogRatioError = error of the log ratio calculated according to the error model chosen.	
#PValueLogRatio = Significance level of the Log Ratio computed for a feature.	
#gProcessedSignal = Dye-normalized signal after surrogate "algorithm," green "channel," used for computation of log ratio.	
#rProcessedSignal = Dye-normalized signal after surrogate "algorithm," red "channel," used for computation of log ratio.	
!sample_table_begin	
ID_REF	VALUE	LogRatioError	PValueLogRatio	gProcessedSignal	rProcessedSignal
1	-0.7837546	1.30E-01	1.70E-09	2.10E+03	3.46E+02
2	0.3797837	1.15E+00	7.41E-01	5.59E+01	1.34E+02
3	0.2079269	5.38E-02	1.12E-04	5.04E+03	8.14E+03
4	-0.4730291	6.71E-02	1.86E-12	5.66E+03	1.91E+03
5	-0.9481128	1.19E-01	1.30E-15	3.10E+03	3.49E+02
6	-0.0159867	1.33E-01	9.05E-01	8.45E+02	8.14E+02
7	-0.819922	1.14E-01	7.01E-13	2.75E+03	4.16E+02
8	-0.1559774	9.16E-01	8.65E-01	1.34E+02	9.34E+01
9	0.145267	3.90E+00	1.00E+00	2.22E+01	3.10E+01
10	0.3611211	3.40E-01	2.88E-01	1.97E+02	4.52E+02
11	0.5092089	4.39E-01	2.46E-01	1.24E+02	4.01E+02
12	0.3715387	1.69E+00	8.26E-01	3.84E+01	9.04E+01
13	0.1734934	3.57E-01	6.27E-01	2.37E+02	3.53E+02
14	-0.9340707	1.20E-01	6.90E-15	2.96E+03	3.45E+02
15	-0.2956317	5.78E-01	6.09E-01	2.46E+02	1.25E+02
16	-0.2321102	1.22E+00	8.49E-01	1.09E+02	6.37E+01
17	-0.1603561	1.16E+00	8.90E-01	1.06E+02	7.34E+01
18	-0.5063897	1.63E-01	1.95E-03	1.15E+03	3.58E+02
19	0.1990761	1.32E-01	1.32E-01	6.65E+02	1.05E+03
20	0.2985912	8.89E-01	7.37E-01	8.06E+01	1.60E+02
!sample_table_end