title: US1 (R) Hsab-08-62

description:
aRNA:	US1
Array ID:	Hsab-08-62
Patient&sample ID:	US11
Sex:	female
Basic disease:	ischemic cardiomyopathy
Days after Tx:	11y
Histology (ISHLT grade):	3A
Clinical history notes:	transplanted more than 11 years ago, patient stopped to take immunosuppression for about 1 year before this rejection
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 16 (R) Hsab-04-50

status: Public on Oct 24 2005

type: RNA

city: Bethesda

first: Natalia

last: Shulzhenko

state: MD

address: 9000 Rockville Pike, Building 4, room 111

department: NIAID

country: USA

institute: NIH

description:
aRNA: 16
Patient&sample ID:	Y90
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	90
Histology (ISHLT grade):	3A
Clinical history notes:	1 month after anti-rejection pulse
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-04

molecule: total RNA

organism: Homo sapiens

source_name: reference pool, Cy5

source_name: endomyocardial biopsy, Cy3


title: 87 (pre-Ch) Hsab-08-46

description:
aRNA:	87
Array ID:	Hsab-08-46
Patient&sample ID:	AA27
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	27
Histology (ISHLT grade):	0
Clinical history notes:	42 days before Chagas disease reactivation
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 38 (N) Hsab-04-56

description:
aRNA: 38
Array ID:	Hsab-04-56
Patient&sample ID:	U14
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	14
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-04


title: 70 (N) Hsab-08-59

description:
aRNA:	70
Array ID:	Hsab-08-59
Patient&sample ID:	Q58
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	58
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 71 (pre-Ch) Hsab-08-77

description:
aRNA:	71
Array ID:	Hsab-08-77
Patient&sample ID:	F21
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	21
Histology (ISHLT grade):	0
Clinical history notes:	61 days before Chagas disease reactivation
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 80 (Ch) Hsab-08-00

description:
aRNA: 	80
Array ID:	Hsab-08-00
Patient&sample ID:	H86
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	86
Histology (ISHLT grade):	Ch
Clinical history notes:	starting anti-Chagas treatment
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 86 (pre-Ch) Hsab-08-45

description:
aRNA:	86
Array ID:	Hsab-08-45
Patient&sample ID:	H24
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	24
Histology (ISHLT grade):	0
Clinical history notes:	62 days before Chagas disease reactivation
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 24 (R) Hsab-04-54

description:
aRNA: 24
Patient&sample ID:	Y538
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	538
Histology (ISHLT grade):	0
Clinical history notes:	patient presented clinical sign of rejection (flutter), anti-rejection treatment
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-04


title: 32 (N) Hsab-04-55

description:
aRNA: 32
Patient&sample ID:	K38
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	38
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-04


title: 26 (N) Hsab-04-53

description:
aRNA: 26
Patient&sample ID:	L69
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	69
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-04


title: 76 (Ch) Hsab-08-78

description:
aRNA:	76
Array ID:	Hsab-08-78
Patient&sample ID:	A72
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	72
Histology (ISHLT grade):	Ch
Clinical history notes:	starting anti-Chagas treatment
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 34 (N) Hsab-03-82

description:
aRNA 34
Patient&sample ID:	P17
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	17
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 42 (N) Hsab-03-79

description:
aRNA:42
Patient&sample ID:	Q113
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	113
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 40 (N) Hsab-04-58

description:
aRNA: 	40
Array ID:	Hsab-04-58
Patient&sample ID:	S46
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	46
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-04


title: 31 (N) Hsab-03-81

description:
aRNA: 31
Patient&sample ID:	C60
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	60
Histology (ISHLT grade):	1A
Clinical history notes:	3 months before leprosy
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 15 (R) Hsab-03-71

description:
aRNA: 15
Patient&sample ID:	N25
Sex:	female
Basic disease:	ischemic cardiomyopathy
Days after Tx:	25
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 37 (N) Hsab-03-77

description:
aRNA: 37
Patient&sample ID:	T54
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	54
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 35 (N) Hsab-03-72

description:
aRNA: 35
Patient&sample ID:	P59
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	59
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 34 (N) Hsab-03-67

description:
aRNA:34
Patient&sample ID:	P17
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	17
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 28 (Pre-R) Hsab-03-69

description:
aRNA: 28
Patient&sample ID:	AE41
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	41
Histology (ISHLT grade):	0
Clinical history notes:	14days before Quilty B and 1B rejection
Final Clinical diagnosis:	Pre-R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: flox2_2_TSA_DP

city: Memphis

first: Paul

middle: K.

last: Brindle

state: TN

address: 332 N Lauderdale

department: Biochemistry

institute: St Jude Children's Research Hospital

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572820040206400907920925
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.466100215912,SFGene:All
Background:Avg:102.05,Stdev:2.01,Max:107.8,Min:96.9
Noise:Avg:6.89,Stdev:0.27,Max:7.8,Min:6.3
RawQ:3.64
Corner+:Avg:476,Count:32
Corner-:Avg:9501,Count:32
Central-:Avg:10469,Count:9

data_processing: standard Affymetrix protocols

label: biotin

organism: Mus musculus

source_name: primary mouse embryonic fibroblasts

tag: CBP, p300, CH1, TAZ1, dipyridyl, hypoxia mimetic, Trichostatin A, TSA, MEF


title: 22 (N) Hsab-03-70

description:
aRNA: 22
Patient&sample ID:	C147
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	147
Histology (ISHLT grade):	3A
Clinical history notes:	2 weeks before cutaneous and 2 months before cardiac leprosy
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 31 (N) Hsab-03-66


title: flox1_TSA_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of CBP and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920962
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.376535415649,SFGene:All
Background:Avg:180.02,Stdev:14.38,Max:209.8,Min:142.7
Noise:Avg:12.76,Stdev:1.13,Max:15.9,Min:10.6
RawQ:6.49
Corner+:Avg:589,Count:32
Corner-:Avg:8509,Count:32
Central-:Avg:9575,Count:9


title: triCH1flox2_2_TSA_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920964
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.200486660004,SFGene:All
Background:Avg:132.97,Stdev:4.77,Max:143.9,Min:119.0
Noise:Avg:9.03,Stdev:0.47,Max:10.8,Min:8.1
RawQ:4.65
Corner+:Avg:485,Count:32
Corner-:Avg:9198,Count:32
Central-:Avg:10505,Count:9


title: triCH1flox1_TSA_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP. The remaining allele of CBP was a conditional knock out allele. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572820040206400907920895
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:6.185513496399,SFGene:All
Background:Avg:105.35,Stdev:3.00,Max:112.9,Min:97.3
Noise:Avg:6.77,Stdev:0.24,Max:7.6,Min:6.2
RawQ:3.71
Corner+:Avg:370,Count:32
Corner-:Avg:8583,Count:32
Central-:Avg:9942,Count:9


title: triCH1flox2_2_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920982
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.942280769348,SFGene:All
Background:Avg:122.48,Stdev:4.58,Max:132.1,Min:106.4
Noise:Avg:9.04,Stdev:0.49,Max:10.1,Min:7.1
RawQ:3.96
Corner+:Avg:455,Count:32
Corner-:Avg:9047,Count:32
Central-:Avg:10165,Count:9


title: flox1_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of CBP and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920973
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.748036861420,SFGene:All
Background:Avg:180.20,Stdev:3.47,Max:188.2,Min:168.2
Noise:Avg:13.38,Stdev:0.40,Max:14.7,Min:12.5
RawQ:5.86
Corner+:Avg:674,Count:32
Corner-:Avg:8193,Count:32
Central-:Avg:9459,Count:9


title: 29 Hsab-03-58

description:
aRNA:29
Patient&sample ID:	W63
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	63
Histology:	toxoplasma myocarditis
Clinical history notes:	anti-toxoplasma treatment
Final Clinical diagnosis:	toxoplasma myocarditis
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 70 (N) Hsab-08-26

description:
aRNA:	70
Array ID:	Hsab-08-26 Patient&sample ID:	Q58
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	58
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 25 (pre-Ch) Hsab-03-64

description:
aRNA: 25
Patient&sample ID:	A7
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	7
Histology (ISHLT grade):	0
Clinical history notes:	65 days before cardiac reactivation of Chagas
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 18 (R) Hsab-03-54

description:
aRNA: 18
Patient&sample ID:	Z15
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	15
Histology (ISHLT grade):	3B
Clinical history notes:	anti-rejection treatment
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: triCH1flox1_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP. The remaining allele of CBP was a conditional knock out allele. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572820040206400907920905
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.238101482391,SFGene:All
Background:Avg:129.93,Stdev:3.11,Max:139.4,Min:118.6
Noise:Avg:9.03,Stdev:0.29,Max:9.7,Min:8.4
RawQ:4.76
Corner+:Avg:525,Count:32
Corner-:Avg:9326,Count:32
Central-:Avg:10178,Count:9


title: flox2_2_DP

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then with 100um dipyridyl (DP) after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920975
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.371708393097,SFGene:All
Background:Avg:154.27,Stdev:8.66,Max:176.4,Min:134.1
Noise:Avg:11.00,Stdev:0.72,Max:13.3,Min:9.2
RawQ:5.08
Corner+:Avg:435,Count:32
Corner-:Avg:8552,Count:32
Central-:Avg:10053,Count:9


title: flox1_TSA

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of CBP and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920947
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.720140933990,SFGene:All
Background:Avg:235.28,Stdev:12.10,Max:255.6,Min:194.1
Noise:Avg:17.27,Stdev:0.89,Max:19.6,Min:15.2
RawQ:8.28
Corner+:Avg:837,Count:32
Corner-:Avg:10238,Count:32
Central-:Avg:11412,Count:9


title: triCH1flox2_2_EtOH

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then again with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920970
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.084809780121,SFGene:All
Background:Avg:144.19,Stdev:4.64,Max:159.9,Min:135.3
Noise:Avg:12.01,Stdev:0.52,Max:13.6,Min:10.8
RawQ:5.03
Corner+:Avg:581,Count:32
Corner-:Avg:10081,Count:32
Central-:Avg:11495,Count:9


title: 36 (N) Hsab-03-56

description:
aRNA: 36
Patient&sample ID:	T19
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	19
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 41 (N) Hsab-03-60

description:
aRNA: 41
Patient&sample ID:	X8
Sex:	male
Basic disease:	ischemic cardiomyopathy
Days after Tx:	8
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: triCH1flox1_TSA

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP. The remaining allele of CBP was a conditional knock out allele. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572820040206400907920884
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.186031341553,SFGene:All
Background:Avg:126.69,Stdev:5.06,Max:141.4,Min:117.4
Noise:Avg:9.22,Stdev:0.52,Max:11.0,Min:7.7
RawQ:4.43
Corner+:Avg:477,Count:32
Corner-:Avg:8069,Count:32
Central-:Avg:9445,Count:9


title: 17 (R) Hsab-03-53

description:
aRNA: 17
Patient&sample ID:	A105
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	105
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: flox2_2_TSA

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920972
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.616947650909,SFGene:All
Background:Avg:127.90,Stdev:3.15,Max:137.0,Min:118.1
Noise:Avg:9.60,Stdev:0.42,Max:11.9,Min:8.5
RawQ:4.30
Corner+:Avg:439,Count:32
Corner-:Avg:7108,Count:32
Central-:Avg:9956,Count:9


title: triCH1flox2_2_TSA

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with 100ng/ml Trichostatin A (TSA), then with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920968
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.356330871582,SFGene:All
Background:Avg:197.70,Stdev:8.26,Max:217.5,Min:175.1
Noise:Avg:13.52,Stdev:0.76,Max:15.2,Min:11.4
RawQ:6.68
Corner+:Avg:576,Count:32
Corner-:Avg:8786,Count:32
Central-:Avg:9630,Count:9


title: triCH1flox1_EtOH

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP. The remaining allele of CBP was a conditional knock out allele. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then again with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920977
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.651946067810,SFGene:All
Background:Avg:119.63,Stdev:5.58,Max:140.1,Min:108.7
Noise:Avg:8.53,Stdev:0.69,Max:11.0,Min:7.0
RawQ:4.16
Corner+:Avg:466,Count:32
Corner-:Avg:8956,Count:32
Central-:Avg:9565,Count:9


title: 27 (pre-R) Hsab-03-48

description:
aRNA: 27
Patient&sample ID:	D185
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	185
Histology (ISHLT grade):	0
Clinical history notes:	3 weeks before clinical sign of rejection (flutter); 3 months after starting treatment of Chagas
Final Clinical diagnosis:	Pre-R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: flox2_2_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905873
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.480028152466,SFGene:All
Background:Avg:58.96,Stdev:0.89,Max:59.8,Min:55.4
Noise:Avg:2.99,Stdev:0.10,Max:3.3,Min:2.7
RawQ:2.12
Corner+:Avg:238,Count:32
Corner-:Avg:15550,Count:32
Central-:Avg:14314,Count:9

tag: CBP, p300, CH1, TAZ1, hypoxia, MEF


title: flox1_EtOH

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of CBP and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then again with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920957
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:6.201836109161,SFGene:All
Background:Avg:212.28,Stdev:5.49,Max:224.6,Min:199.2
Noise:Avg:16.12,Stdev:1.00,Max:21.9,Min:13.4
RawQ:6.78
Corner+:Avg:719,Count:32
Corner-:Avg:7956,Count:32
Central-:Avg:9195,Count:9


title: 30 (N) Hsab-03-49

description:
aRNA:30
Patient&sample ID:	AB91
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	91
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: flox2_2_EtOH

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated under normoxia with 5% carbon dioxide at 37 C in a humid chamber with EtOH vehicle, then again with EtOH vehicle after 30min.  3 hrs later, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900572821040206400907920965
Probe Array Lot: 4009079
Expiration Date: Apr 02 2006 12:00AM
Genus:
species:
Strain/Line:
Individual:
Sample Provider:
Sex:
Age:
Developmental State:
Tissue:
Cell Type:
Genetic Modifications:
Genetic Characteristics:
Disease State:
Reference to Clinical Data:
Growth Conditions:
in vivo Treatments:
Tissue Harvesting Method:
Extract Method:
Molecule Type:
Amplification:
Amount:
Label:
Label Incorporation:
Lab Protocol: Affy Protocol
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:2,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:5.412384033203,SFGene:All
Background:Avg:113.38,Stdev:2.23,Max:119.5,Min:108.4
Noise:Avg:7.82,Stdev:0.29,Max:8.8,Min:7.2
RawQ:3.69
Corner+:Avg:392,Count:32
Corner-:Avg:8218,Count:32
Central-:Avg:9823,Count:9


title: flox1_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of CBP and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905877
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.281831741333,SFGene:All
Background:Avg:71.30,Stdev:4.17,Max:77.0,Min:42.2
Noise:Avg:4.17,Stdev:0.17,Max:4.8,Min:3.8
RawQ:2.80
Corner+:Avg:209,Count:32
Corner-:Avg:12535,Count:32
Central-:Avg:12822,Count:9


title: 16 (R) Hsab-03-51

description:
aRNA: 16
Patient&sample ID:	Y90
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	90
Histology (ISHLT grade):	3A
Clinical history notes:	1 month after anti-rejection pulse
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 20 (R) Hsab-03-47

description:
aRNA: 20
Patient&sample ID:	W97
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	97
Histology (ISHLT grade):	2
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: triCH1flox2_1_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold.  Subconfluent MEFs were treated 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905884
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.852353096008,SFGene:All
Background:Avg:64.27,Stdev:1.03,Max:68.6,Min:61.6
Noise:Avg:3.59,Stdev:0.09,Max:3.9,Min:3.4
RawQ:2.43
Corner+:Avg:253,Count:32
Corner-:Avg:12420,Count:32
Central-:Avg:13583,Count:9


title: triCH1flox1_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP. The remaining allele of CBP was a conditional knock out allele. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905872
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.580704689026,SFGene:All
Background:Avg:60.57,Stdev:1.88,Max:66.3,Min:55.2
Noise:Avg:3.12,Stdev:0.15,Max:3.6,Min:2.6
RawQ:2.42
Corner+:Avg:210,Count:32
Corner-:Avg:13232,Count:32
Central-:Avg:13446,Count:9


title: triCH1flox2_2_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold.  Subconfluent MEFs were treated 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905876
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.112417697906,SFGene:All
Background:Avg:57.74,Stdev:0.70,Max:58.9,Min:54.9
Noise:Avg:2.93,Stdev:0.08,Max:3.1,Min:2.8
RawQ:1.99
Corner+:Avg:170,Count:32
Corner-:Avg:12316,Count:32
Central-:Avg:13004,Count:9


title: 14 (R) Hsab-03-31

description:
aRNA:14
Patient&sample ID:	B10
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	10
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 15 (R) Hsab-03-36

description:
aRNA: 15
Patient&sample ID:	N25
Sex:	female
Basic disease:	ischemic cardiomyopathy
Days after Tx:	25
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: flox2_2_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905849
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.783283233643,SFGene:All
Background:Avg:61.56,Stdev:0.92,Max:63.8,Min:58.7
Noise:Avg:3.20,Stdev:0.07,Max:3.4,Min:3.0
RawQ:2.17
Corner+:Avg:190,Count:32
Corner-:Avg:12686,Count:32
Central-:Avg:13062,Count:9


title: flox2_1_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905853
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.346090793610,SFGene:All
Background:Avg:63.86,Stdev:1.08,Max:66.7,Min:60.4
Noise:Avg:3.42,Stdev:0.16,Max:4.4,Min:3.0
RawQ:2.38
Corner+:Avg:215,Count:32
Corner-:Avg:13655,Count:32
Central-:Avg:13685,Count:9


title: triCH1flox2_2_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold.  Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905848
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.453727245331,SFGene:All
Background:Avg:68.01,Stdev:1.13,Max:70.9,Min:65.0
Noise:Avg:3.60,Stdev:0.10,Max:3.9,Min:3.4
RawQ:2.40
Corner+:Avg:213,Count:32
Corner-:Avg:12894,Count:32
Central-:Avg:13307,Count:9


title: flox2_1_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of p300 and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905843
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:2.571648359299,SFGene:All
Background:Avg:72.99,Stdev:1.56,Max:78.7,Min:68.8
Noise:Avg:4.23,Stdev:0.10,Max:4.5,Min:3.9
RawQ:2.81
Corner+:Avg:227,Count:32
Corner-:Avg:14170,Count:32
Central-:Avg:14237,Count:9


title: tri_CH1_hypoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP (tri-CH1). Subconfluent MEFs were treated with 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Experiment User: jmorris
Lot Number: 3002159
Algorithm: Statistical
Corner+ Avg:42, Count:32
Corner- Avg:5181, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.697724,SFGene:All
Background:Avg:45.24,Stdev:4.65,Max:58.7,Min:39.5
Noise:Avg:2.21,Stdev:0.30,Max:2.8,Min:1.6
RawQ:1.50


title: triCH1flox1_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP. The remaining allele of CBP was a conditional knock out allele. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold.  Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905863
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.427855730057,SFGene:All
Background:Avg:61.53,Stdev:0.82,Max:64.3,Min:58.9
Noise:Avg:3.30,Stdev:0.05,Max:3.5,Min:3.2
RawQ:2.40
Corner+:Avg:213,Count:32
Corner-:Avg:12796,Count:32
Central-:Avg:13346,Count:9


title: triCH1flox2_1_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of CBP and one allele of p300. The remaining allele of p300 was a conditional knock out allele.  At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold.  Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905844
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:3.418659210205,SFGene:All
Background:Avg:70.04,Stdev:0.98,Max:73.4,Min:68.2
Noise:Avg:3.75,Stdev:0.07,Max:4.0,Min:3.6
RawQ:2.61
Corner+:Avg:225,Count:32
Corner-:Avg:13301,Count:32
Central-:Avg:13876,Count:9


title: wildtype_hypoxia

description:
Primary wildtype mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos.  Subconfluent MEFs were treated with 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Experiment User: jmorris
Lot Number: 3002159
Algorithm: Statistical
Corner+ Avg:51, Count:32
Corner- Avg:6978, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.730389,SFGene:All
Background:Avg:36.53,Stdev:1.00,Max:38.9,Min:34.8
Noise:Avg:1.90,Stdev:0.14,Max:2.3,Min:1.7
RawQ:1.38


title: flox1_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos bearing one conditional knockout allele of CBP and were infected at passage 3 with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Probe Array Type: Mouse430_2
Barcode: @52002900410450110805400482905859
Probe Array Lot: 4004829
Expiration Date: Nov 08 2005 12:00AM
Experiment User: jmorris
Algorithm: Statistical
HZ:4 VZ:4,BG:4,SmoothFactorBG:100,Epsilon:0.5,BF:,Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0025,Gamma1L:0.0025,Gamma2H:0.003,Gamma2L:0.003,Perturbation:1.1,TGT:500,NF:1.000000000000,SF:4.069585800171,SFGene:All
Background:Avg:66.60,Stdev:2.13,Max:71.8,Min:59.9
Noise:Avg:3.68,Stdev:0.11,Max:4.1,Min:3.3
RawQ:2.72
Corner+:Avg:231,Count:32
Corner-:Avg:13054,Count:32
Central-:Avg:13157,Count:9


title: tri_CH1_normoxia

description:
Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP (tri-CH1).  Subconfluent MEFs were treated with either 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Experiment User: jmorris
Lot Number: 3002159
Algorithm: Statistical
Corner+ Avg:36, Count:32
Corner- Avg:5956, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.301489,SFGene:All
Background:Avg:33.29,Stdev:0.90,Max:35.8,Min:31.8
Noise:Avg:1.58,Stdev:0.10,Max:1.9,Min:1.4
RawQ:1.21


title: 35 (N) Hsab-03-44

description:
aRNA: 35
Patient&sample ID:	P59
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	59
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: 22 (N) Hsab-03-30

description:
aRNA: 22
Patient&sample ID:	C147
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	147
Histology (ISHLT grade):	3A
Clinical history notes:	2 weeks before cutaneous and 2 months before cardiac leprosy
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: wildtype_normoxia

description:
Primary wildtype mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos.   Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Experiment User: jmorris
Lot Number: 3002034
Algorithm: Statistical
Corner+ Avg:88, Count:32
Corner- Avg:13537, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:3.461269,SFGene:All
Background:Avg:40.18,Stdev:1.27,Max:43.6,Min:37.9
Noise:Avg:2.55,Stdev:0.22,Max:3.1,Min:2.2
RawQ:1.58


title: Mixed wild type/mixed o2 dye-swap rep2 array1

status: Public on Oct 22 2005

city: Ames

first: Hongwu

last: Jia

state: IA

address: 1407 Agronomy Hall

department: Agronomy

institute: Iowa State University

description: The channel 1 and channel 2 images were analyzed using ImaGene 4.1 software (BioDiscovery, Marina Del Rey, CA) to obtain average signal and background intensities for each spot.

scan_protocol: The slide was scanned using a laser scanner (ScanArray 5000, GSI Lumonics- Packard BioScience, Billerica, MA) for both channel 1 (Cy3) and 2 (Cy5) at 10 um resolution.

data_processing: The control and empty spots were removed first. The background of each spot was subtracted from the signal, and then the background-subtracted signal intensity of duplicate spots within each slide was averaged. LOWESS normalization was used to remove the dye bias. The log ratio of normalized CH1 and CH2 was calculated.

molecule: polyA RNA

organism: Zea mays

source_name: Mixed 8 wild type lines endosperm 14 DAP

extract_protocol: mRNA was extracted from the frozen immature endosperm tissue with the PolyATract System 1000 mRNA isolation kit (Promega, Madison, WI) according to the manufacturer's instructions.

tag: Lines

value: A619 wild type, B14A wild type, B45 wild type, B46 wild type, B57 wild type, B66 wild type, B73 wild type, and M14 wild type

tag: Tissue

value: Endosperm Stage:14 DAP

source_name: Mixed 8 o2 mutant lines endosperm 14 DAP

value: A619 opaque2 mutant, B14A opaque2 mutant, B45 opaque2 mutant, B46 opaque2 mutant, B57 opaque2 mutant, B66 opaque2 mutant, B73 opaque2 mutant, and M14 opaque2 mutant


title: B46/o2 dye-swap rep3 array1

source_name: B46 wild type endosperm 14 DAP

tag: Line

value: B46 wild type

value: Endosperm

tag: Stage

value: 14 DAP

source_name: B46 o2 endosperm 14 DAP

value: B46 opaque2 mutant


title: MA10_BAT_torpor_5a

status: Public on Oct 21 2005

city: Fairbanks

first: Jun

last: Yan

state: AK

address: 311 Irving Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

description: brown adipose tissue from winter torpid arctic ground squirrel

data_processing: Local background median was subtracted from signal median as background-corrected signal. Background-corrected signals were divided by their median on the array as the normalized expression values.

organism: Urocitellus parryii

source_name: brown adipose tissue

value: brown adipose

value: winter torpor


title: 28 (pre-R) Hsab-03-28

description:
aRNA: 28
Patient&sample ID:	AE41
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	41
Histology (ISHLT grade):	0
Clinical history notes:	14days before Quilty B and 1B rejection
Final Clinical diagnosis:	Pre-R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-03


title: M14/o2 dye-swap rep1 array2

data_processing: The control and empty spots were removed first. The background of each spot was subtracted from the signal, and then the background-subtracted signal intensity of duplicate spots within each slide was averaged. LOWESS normalization was used to remove the dye bias. The log ratio of normalized CH2 and CH1 was calculated.

source_name: M14 o2 endosperm 14 DAP

value: M14 opaque2 mutant

source_name: M14 wild type endosperm 14 DAP

extract_protocol: mRNA was extracted from the frozen immature endosperm tissue with the PolyATract System 1000 mRNA isolation kit (Promega, Madison, WI) according to the manufacturer's instructions

value: M14 wild type


title: Mixed wild type/mixed o2 dye-swap rep1 array1


title: Mixed wild type/mixed o2 dye-swap rep3 array2


title: MA10_BAT_torpor_5b


title: B46/o2 dye-swap rep1 array1


title: M14/o2 dye-swap rep2 array2

value: M14 wild type Tissue:Endosperm Stage:14 DAP


title: M14/o2 dye-swap rep3 array2

value: M14 opaque2 mutant Tissue:Endosperm Stage:14 DAP


title: B46/o2 dye-swap rep2 array1


title: B46/o2 dye-swap rep2 array2


title: B46/o2 dye-swap rep1 array2


title: M14/o2 dye-swap rep2 array1


title: Mixed wild type/mixed o2 dye-swap rep1 array2


title: M14/o2 dye-swap rep1 array1


title: Ovaries_MTX_1

city: Kingston

first: Joslynn

middle: Gayle

last: Affleck

state: ON

address: 116 Barrie St.

department: Biology

country: Canada

institute: Queen's University

description: Comparision between untreated and MTX treated ovaries.

data_processing: Normalized by overall median adjustment

organism: Drosophila melanogaster

source_name: Methotrexate treated ovaries

tag: MTX treated ovaries dissected from adult flies.

source_name: Untreated ovaries

tag: Untreated ovaries from adult flies


title: Ovaries_MTX_2

tag: Untreated ovaries

tag: MTX treated ovaries dissected from adult flies


title: Mixed wild type/mixed o2 dye-swap rep2 array2


title: B46/o2 dye-swap rep3 array2


title: M14/o2 dye-swap rep3 array1


title: S3_MTX_2

description: Comparision between untreated and MTX treated S3 cells.

source_name: Untreated S3 Drosophila Cells

tag: Untreated S3 cells

source_name: Methotrexate treated S3 cells

tag: MTX exposed S3 cells


title: Mixed wild type/mixed o2 dye-swap rep3 array1


title: S3_MTX_4

source_name: Methotrexate treated S3 Drosophila Cells

tag: MTX treated S3 cells


title: S3_MTX_3


title: MA10_BAT_torpor_4


title: S3_MTX_1

source_name: Untreated S3 Drosophila cells

source_name: Methotrexate treated S3 Drosophila cells


title: MA10_BAT_torpor_3


title: MA10_BAT_summer_3

description: brown adipose tissue from summer active arctic ground squirrel

value: summer active in August


title: MA10_BAT_torpor_1


title: MA10_BAT_summer_2b


title: MA10_BAT_torpor_2


title: MA10_BAT_summer_1a


title: MA07_BAT_torpor_5a

data_processing: background median was subtracted from signal median as background-corrected signal. Background-corrected signals were divided by their median on the array as the normalized expression values.


title: MA07_BAT_summer_1b

data_processing: Background median was subtracted from signal median as background-corrected signal. Background-corrected signals were divided by their median on the array as the normalized expression values.


title: MA07_BAT_torpor_3


title: MA11_BAT_torpor_4


title: MA10_BAT_summer_1b


title: MA11_BAT_torpor_5a


title: MA07_BAT_summer_2b


title: MA07_BAT_summer_1a

source_name: Brown adipose tissue in summer

value: Brown adipose


title: MA11_BAT_summer_3


title: MA11_BAT_torpor_5b


title: MA07_BAT_summer_3


title: MA07_BAT_torpor_5b


title: MA07_BAT_torpor_2


title: MA11_BAT_torpor_3


title: MA07_BAT_torpor_1


title: MA11_BAT_summer_2a


title: MA10_BAT_summer_2a


title: MA07_BAT_summer_2a


title: MA07_BAT_torpor_4


title: MA11_BAT_torpor_1


title: MA11_BAT_summer_1b


title: MA11_BAT_summer_1a


title: MA08_BAT_torpor_3


title: MA08_BAT_torpor_5a


title: MA08_BAT_torpor_4


title: MA11_BAT_summer_2b


title: MA08_BAT_summer_1a


title: MA08_BAT_torpor_5b


title: MA08_BAT_summer_1b


title: MA08_BAT_summer_2b


title: Adenoviral infected fibroblasts Mu11kA- 0493

status: Public on Oct 20 2005

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Quiescent C57/Bl6 fibroblasts were Ad (E1-E3-LacZ) infected for 16hrs.  RNA was then harvested, transcribed to cDNA, and hybridized to a Mu11kA array.

hyb_protocol: The cDNA was fragmented before hybridization, and we prepared a hybridization cocktail that included the fragmented cDNA, probe array controls, bovine serum albumin and herring sperm DNA. We hybridized the cDNA to the oligonucleotide probes on the probe array for a 16-h incubation at 45 °C. Immediately after the hybridization, the hybridized probe array underwent an automated washing and staining protocol on an Affymetrix fluidics station.

scan_protocol: We scanned the DNA chips with the Affymetrix GeneChip scanner and processed the signals by the GeneChip expression analysis algorithm (v.2; Affymetrix).

data_processing: Imported into genespring and normalized per chip by 50th percentile and by gene by median expression

label: bitotin-labeled

source_name: Adenoviral infected quiescent fibroblasts

label_protocol: We generated biotin-labeled cDNA by in vitro transcription from the RNA.

extract_protocol: Trizol

treatment_protocol: Primary wildtype mouse embryo fibroblasts were prepared from 13.5 dpc C57Bl/6 embryos

tag: C57/Bl6 MEFs

tag: passage 3

tag: serum starved for 48 hrs.

tag: E1- LacZ Ad infected for 16 hrs.


title: MA08_BAT_summer_2a


title: MA11_BAT_torpor_2


title: MA08_BAT_summer_3


title: Quiescent Fibroblast Mu11kA- 370

description: Quiescent C57/Bl6 fibroblasts were mock infected for 16hrs.  RNA was then harvested, transcribed to cDNA, and hybridized to a Mu11kA array.

label: biotin-labeled

source_name: Quiescent Mock infected Fibroblasts

treatment_protocol: Primary wildtype mouse embryo fibroblasts were prepared from 13.5 dpc C57Bl/6 embryos.

tag: mock infected for 16 hrs.


title: MA08_BAT_torpor_2


title: Adenoviral infected fibroblasts Mu11kA- 0054

hyb_protocol: The cRNA was fragmented before hybridization, and we prepared a hybridization cocktail that included the fragmented cRNA, probe array controls, bovine serum albumin and herring sperm DNA. We hybridized the cRNA to the oligonucleotide probes on the probe array for a 16-h incubation at 45 °C. Immediately after the hybridization, the hybridized probe array underwent an automated washing and staining protocol on an Affymetrix fluidics station.

treatment_protocol:
Primary wildtype mouse embryo fibroblasts were prepared from 13.5 dpc C57Bl/6 embryos
Infected with a 1st Generation E1-E3- LacZ (under CMV promoter) Adenovirus
RNA harvested 16 hours post infection


title: Adenoviral infected fibroblasts Mu11kA- 1169


title: Adenoviral infected fibroblasts Mu11kA- 1168


title: Quiescent Fibroblast Mu11kA- 346


title: Quiescent Fibroblast Mu11kA- 299

source_name: Mock infected quiescent fibroblasts

tag: taken at passage 3

tag: mock infected for 16hrs.


title: prp43 G429A COLD SHIFT_rev

city: Santa Cruz

first: Roland

middle: J

last: Nagel

state: CA

address: Sinsheimer Labs

institute: UCSC

description: Burckin et al., Nat Struct Mol Biol. 2005 Feb;12(2):175-82

scan_protocol: GENEPIX SOFTWARE

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: YEPD rich media

treatment_protocol: WT cold shift 16C 60 mins

tag: WT

treatment_protocol: prp43 G429A cold shift 16C 60 mins

tag: prp43 G429A


title: Quiescent Fibroblast Mu11kA- 343


title: Quiescent Fibroblast Mu11kA- 250

description: Quiescent C57/Bl6 fibroblasts were mock infected for 16hrs.  RNA was then harvested, in vitro transcribed to cDNA, and hybridized to a Mu11kA array.

treatment_protocol:
Primary wildtype mouse embryo fibroblasts were prepared from 13.5 dpc C57Bl/6 embryos.
After thawing, the cells were passaged once in DMEM and 15% HIFBS then rendered quiescent in DMEM and 0.2% HIFBS for 48 hours.
Mock infected with for 16 hours in DMEM, 25mMHepes, pH7.6.

tag: C57/Bl6 murine embroynic fibroblasts

tag: Quiescent (48hrs. minimal serum media)

tag: total RNA


title: Adenoviral infected fibroblasts Mu11kA- 0183


title: Quiescent Fibroblast Mu11kA- 302


title: Adenoviral infected fibroblasts Mu11kB- 0493

description: Quiescent C57/Bl6 fibroblasts were Ad (E1-E3-LacZ) infected for 16hrs.  RNA was then harvested, transcribed to cDNA, and hybridized to a Mu11kB array.


title: Adenoviral infected fibroblasts Mu11kA- 0114


title: Adenoviral infected fibroblasts Mu11kB- 1168


title: prp43 G429A COLD SHIFT

scan_protocol: GENEPIX SOFTWARE AXON SCANNER

data_processing: Burckin et al., Nat Struct Mol Biol. 2005 Feb;12(2):175-82

treatment_protocol: WT cold shift 16C  60 mins


title: MA08_BAT_torpor_1

tag: Tissue

tag: Stage


title: Adenoviral infected fibroblasts Mu11kB- 1169


title: Quiescent Fibroblast Mu11kB- 302


title: Adenoviral infected fibroblasts Mu11kB- 0183


title: prp43 S247A COLD SHIFT_rev

source_name: S cerivisiae

treatment_protocol: prp43 S247A cold shift 16C 60 mins

tag: prp43 S247A


title: Adenoviral infected fibroblasts Mu11kB- 0114


title: prp43 S247A COLD SHIFT

scan_protocol: GENEPIX SOFTWARE AXON  SCANNER

source_name: WT cold shift_16C_60 mins

source_name: prp43 S247A


title: Quiescent Fibroblast Mu11kB- 346


title: Quiescent Fibroblast Mu11kB- 299


title: Quiescent Fibroblast Mu11kB- 370


title: Adenoviral infected fibroblasts Mu11kB- 0054


title: Quiescent Fibroblast Mu11kB- 343


title: 0hCy5_X_120hCy3_Exp1_Repl2

status: Public on Oct 19 2005

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of a time-course experiment aimed at evaluating gene expression modulation during the mycelium-to-yeast dimorphic shift in P. brasiliensis

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardt�s solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS, 50% formamide and 92,5 ng/ul poly (dT) 25u (Amersham). Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

data_processing: Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with less than 50% of the pixels with values lower than the median local background plus two SD have been flagged and excluded from further analyses. Raw data were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array

organism: Paracoccidioides brasiliensis

label_protocol: The RNA sample extracted with Trizol was further purified with aid of the RNA easy kit (Qiagen) and labeled by incorporation of Cy3- or Cy5-dCTP. Briefly, 30 ug of total P. brasiliensis RNA were mixed with 2 ug of oligo(dT)12-18 in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy3-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 120 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

extract_protocol: Yeast cells and mycelium were disrupted with glass beads and grinding in liquid nitrogen, respectively, and immediately mixed with Trizol (Gibco-BRL) for RNA extraction following the supplier�s recommendations. To verify the RNA integrity, twenty micrograms of RNA from each treatment were fractionated in 2.2-M formaldehyde, 1.2 % agarose gel, stained with ethidium bromide, and visualized with UV-light. The presence of intact 28S and 18S ribosomal RNA bands was used as a criterion to verify if the RNA was intact. RNAse-free DNA-se treatment was done in a final volume of 100 ul, containing 40 mM Tris-HCl pH 7.5 and 6 mM MgCl2, 1 ul of RNAsin (40 U/ul, Promega, USA), 10 ul of RNAse-free DNAse (1 U/ul, Promega or Life Technologies, USA), 2.5 ul of 200 mM DTT, and 10 mg of total RNA. The reaction was incubated at 37oC for 60 min and stopped by incubating at 70oC for 30 min. The absence of DNA contamination after the RNAse-free DNAse treatment was verified by PCR-amplification of the GP43 gene

treatment_protocol: 120-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 120 hours, when cells were harvested for RNA purification.

label_protocol: The RNA sample extracted with Trizol was further purified with aid of the RNA easy kit (Qiagen) and labeled by incorporation of Cy3- or Cy5-dCTP. Briefly, 30 ug of total P. brasiliensis RNA were mixed with 2 ug of oligo(dT)12-18 in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy5-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium was cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) at 26oC (mycelium phase). To obtain mycelium cultures, yeast cells were recovered from the lungs of intratracheally infected mice and sub-cultured 3 successive times in mYPD slants, at 10-day intervals. In order to obtain the fungal mycelium phase, slant yeast cells were inoculated in 200 ml of the same medium and incubated at 26oC for approximately 9 days under shaking, when 100% of conversion was achieved.


title: 0hCy5_X_72hCy3_Exp2_Repl1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 90% PMT gain

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 72 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 72-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 72 hours, when cells were harvested for RNA purification.

growth_protocol: Fungal mycelium was cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) at 26oC (mycelium phase). To obtain mycelium cultures, yeast cells were recovered from the lungs of intratracheally infected mice and sub-cultured 3 successive times in mYPD slants, at 10-day intervals. In order to obtain the fungal mycelium phase, slant yeast cells were inoculated in 200 ml of the same medium and incubated at 26oC for approximately 9 days under shaking, when 100% of conversion was achieved.


title: 0hCy5_X_48hCy3_Exp1_Repl2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 70% PMT gain

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 48 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 48-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 48 hours, when cells were harvested for RNA purification.


title: Quiescent Fibroblast Mu11kB- 250

tag: C57/Bl6 MEFs

tag: passage 3

tag: serum starved for 48 hrs.


title: 0hCy5_X_72hCy3_Exp2_Repl2


title: 0hCy5_X_120hCy3_Exp2_Repl1


title: 0hCy5_X_48hCy3_Exp2_Repl2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 70% PMT gain


title: 0hCy5_X_120hCy3_Exp2_Repl2


title: 0hCy5_X_48hCy3_Exp2_Repl1


title: 0hCy5_X_5hCy3_Exp1_Repl2

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardt´s solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS, 50% formamide and 92,5 ng/ul poly (dT) 25u (Amersham). Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 75% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 5 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

extract_protocol: Yeast cells and mycelium were disrupted with glass beads and grinding in liquid nitrogen, respectively, and immediately mixed with Trizol (Gibco-BRL) for RNA extraction following the supplier’s recommendations. To verify the RNA integrity, twenty micrograms of RNA from each treatment were fractionated in 2.2-M formaldehyde, 1.2 % agarose gel, stained with ethidium bromide, and visualized with UV-light. The presence of intact 28S and 18S ribosomal RNA bands was used as a criterion to verify if the RNA was intact. RNAse-free DNA-se treatment was done in a final volume of 100 ul, containing 40 mM Tris-HCl pH 7.5 and 6 mM MgCl2, 1 ul of RNAsin (40 U/ul, Promega, USA), 10 ul of RNAse-free DNAse (1 U/ul, Promega or Life Technologies, USA), 2.5 ul of 200 mM DTT, and 10 mg of total RNA. The reaction was incubated at 37oC for 60 min and stopped by incubating at 70oC for 30 min. The absence of DNA contamination after the RNAse-free DNAse treatment was verified by PCR-amplification of the GP43 gene

treatment_protocol: 5-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 5 hours, when cells were harvested for RNA purification.

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium was cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) at 26oC (mycelium phase). To obtain mycelium cultures, yeast cells were recovered from the lungs of intratracheally infected mice and sub-cultured 3 successive times in mYPD slants, at 10-day intervals. In order to obtain the fungal mycelium phase, slant yeast cells were inoculated in 200 ml of the same medium and incubated at 26oC for approximately 9 days under shaking, when 100% of conversion was achieved.


title: 0hCy5_X_24hCy3_Exp2_Repl1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 100% PMT gain

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 24 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 24-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 24 hours, when cells were harvested for RNA purification.


title: 0hCy5_X_72hCy3_Exp1_Repl1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain


title: 0hCy5_X_120hCy3_Exp1_Repl1


title: 0hCy5_X_72hCy3_Exp1_Repl2


title: 0hCy5_X_48hCy3_Exp1_Repl1


title: 0hCy5_X_24hCy3_Exp1_Repl2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 100% PMT gain


title: 0hCy5_X_24hCy3_Exp2_Repl2


title: 0hCy5_X_5hCy3_Exp1_Repl1


title: 0hCy3_X_48hCy5_Exp2_Repl2

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 48 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_72hCy5_Exp1_Repl1

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 72 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_72hCy5_Exp1_Repl2


title: 0hCy3_X_120hCy5_Exp1_Repl2

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 120 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_120hCy5_Exp1_Repl1


title: 0hCy3_X_120hCy5_Exp2_Repl2


title: 0hCy3_X_72hCy5_Exp2_Repl2


title: 0hCy3_X_72hCy5_Exp2_Repl1


title: 0hCy3_X_48hCy5_Exp1_Repl1


title: 0hCy3_X_48hCy5_Exp2_Repl1


title: 0hCy3_X_120hCy5_Exp2_Repl1


title: 0hCy3_X_24hCy5_Exp2_Repl2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 90% PMT gain

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, São Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 24 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_24hCy5_Exp1_Repl2


title: 0hCy3_X_48hCy5_Exp1_Repl2


title: 0hCy3_X_24hCy5_Exp1_Repl1


title: 0hCy3_X_24hCy5_Exp2_Repl1


title: 0hCy3_X_10hCy5_Exp1_Repl2

growth_protocol: Fungal mycelium, cultivated in mYPDfor 9 days, at 26oC was transfered to 37oC for a period of 10 hours, at 120 rpm in a rotatory shaker, when cells were harvested for RNA purification.

treatment_protocol: 10-hour incubation at 37oC in mYPD, at 120 rpm in a rotatory shaker

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 10 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_5hCy5_Exp1_Repl2

tag: We used P. brasiliensis isolate 18, named Pb18 (provided by Dr. Z. P. Camargo, UNIFESP, S�o Paulo, Brazil). Fungal mycelium, cultivated in modified YPD medium (mYPD, 0.5% yeast extract, 0.5% casein peptone, 1.5% glucose, pH6.5) for 9 days, at 26oC was transfered to 37oC for a period of 5 hours, when cells were harvested for RNA purification.


title: 0hCy3_X_5hCy5_Exp2_Repl1


title: 0hCy3_X_10hCy5_Exp2_Repl1


title: 0hCy3_X_5hCy5_Exp2_Repl2


title: Col_+IAA_3

city: Albany

first: Yoko

last: Okushima

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center, U. C. Berkeley

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 3

organism: Arabidopsis thaliana

source_name: Light grown liquid cultured seedlings (7-day old)