title: Rice Bala 0ppm Arsenate (Control) Rep1

city: Aberdeen

first: Gareth

last: Norton

address: St Machar drive

department: Plant and Soil Science

country: United Kingdom

institute: University of Aberdeen

description: Gene expression data from rice roots (variety Bala) grown in hydroponics for one week with 0ppm arsenate, rep1

hyb_protocol: Hybridisation, washing and staining procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.

scan_protocol: Scanning procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: Rice Hydroponic Roots 1 Week Old

label_protocol: RNA was processed for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. Briefly, 5 ug of total RNA was used in the one-cycle cDNA synthesis reaction. After the generation of double stranded cDNA an in vitro transcription reaction was performed to generate biotinylated cRNA. (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: 100 mg of root material was pooled from four separate plants and RNA was extracted using the TRIzol method (Invitrogen) followed by further purification and DNase treatment using the RNeasy clean up kit (Qiagen).

treatment_protocol: Germinated seedlings were grown for 1 week in hydroponics with 0ppm arsenate under 12 hr of light as described in Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49

tag: Rice variety Bala, 1 week in hydroponics, whole root system


title: astrocytes hypoxia batch 3

status: Public on Mar 16 2006

type: RNA

city: New York

first: Sarah

last: Mense

state: NY

address: 722 West 168th Street

department: Environmental Health Sciences

country: USA

institute: Columbia University

description: astrocytes from second trimester (14-19 weeks) human fetal brains

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: astrocyte

tag: astrocytes from second trimester human fetal brains


title: astrocytes hypoxia batch 1


title: Normal diaphragm 4, 8 week

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Standard Affymetrix

data_processing: Affymetrix MAS 5.0 software

label: Standard Affymetrix

organism: Mus musculus

source_name: Control mouse for dy/dy, 8 week

tag: 8 week old control mouse diaphragm


title: HVSMC_ Thapsigargin_treated_rep2

city: Burlington

first: Anjanette

middle: D

last: Watson

state: VT

address: 120A Marsh Life Science

department: Bioinformatics Core

institute: University of Vermont

description: each of three experiments cell cultures were split three ways; one of the resulting samples was left untreated (C), another was treated with thapsigargin (TG), and the third was treated with elevated K+ (K)

scan_protocol: The probe arrays were scanned (Hewlett-Packard GeneArray Scanner, Agilent Technologies, Inc.) to quantify the fluorescence intensity associated with each oligonucleotide probe.

data_processing: RMA

label: biotin-labeled

source_name: human cerebral artery

label_protocol: Double-stranded cDNA was then synthesized followed by an in vitro transcription reaction and fragmentation reaction to produce biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr

growth_protocol: hcVSMCs and rat VSMCs (passages 2-4) were grown to approximately 60% confluence and serum starved in DMEM containing 0.1% FBS 24-48 hr prior to treatment

extract_protocol: Total RNA was extracted from treated hc VSMCs using TriZol reagent and chloroform.  RNA was precipitated using isoproponol and glycoblue, washed with 75% ethanol, dissolved in RNAse free water and quantified using the NanoDrop® spectrophotometer.

treatment_protocol: Early passage hcVSMCs (passage 2-4) were obtained from human cerebral artery explants. Briefly, 2 mm slices of human pial artery (IRB# CHRMS 01-195; informed consent) were applied to scored 60 mm culture dishes, cultured in SMGM2 media (Cambrex Bio Science, Hopkinton, MA), and passaged with trypsin/EDTA. For hypoxia exposure, cells were incubated at 2% O2 by N2 injection into a humidified CO2 incubator (Forma, Marietta, OH). NOC-18, Cu/Zn superoxide dismutase (SOD), catalase, xanthine, and xanthine oxidase were obtained from Calbiochem (San Diego, CA). S-nitroso-L-glutathione (GSNO) was obtained from Alexis

tag: Gender

value: Male

tag: Age

value: 45 years

tag: Tissue

value: human cerebral artery


title: Rice Azucena 1ppm Arsenate Rep2

description: Gene expression data from rice roots (variety Azucena) grown in hydroponics for one week with 1ppm arsenate, rep2

treatment_protocol: Germinated seedlings were grown for 1 week in hydroponics with 1ppm arsenate under 12 hr of light as described in Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49

tag: Rice variety Azucena, 1 week in hydroponics with 1ppm arsenate, whole root system


title: Rice Bala 0ppm Arsenate (Control) Rep2

description: Gene expression data from rice roots (variety Bala) grown in hydroponics for one week with 0ppm arsenate, rep2

growth_protocol: Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49


title: HVSMC_Control_rep3

hyb_protocol: biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr


title: Rice Bala 1ppm Arsenate Rep1

description: Gene expression data from rice roots (variety Bala) grown in hydroponics for one week with 1ppm arsenate, rep1

tag: Rice variety Bala, 1 week in hydroponics with 1ppm arsenate, whole root system


title: HeLa hypoxia batch 3

source_name: HeLa

tag: Human cervical cancer cells


title: HeLa hypoxia batch 1


title: astrocytes normoxia batch 1


title: HSVMC_HighK+_rep2

source_name: cerebral artery


title: Rice Bala 1ppm Arsenate Rep2

description: Gene expression data from rice roots (variety Bala) grown in hydroponics for one week with 1ppm arsenate, rep2


title: Normal diaphragm 2, 8 week

description: Standard Affymetrix


title: 1180 (N) Hsac-02-76

status: Public on Mar 15 2006

city: Bethesda

first: Natalia

last: Shulzhenko

state: MD

address: 9000 Rockville Pike, Building 4, room 111

department: NIAID

institute: NIH

description:
aRNA:	1180
Patient&sample ID:	AL11
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	11
Histology:	0
Clinical history notes:
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.

data_processing: Lowess intensity dependent normalization. Log2 Ratio Cy3/Cy5. Filtering applied.

source_name: reference pool

tag: pool of endomyocardial biopsies

source_name: endomyocardial biopsy

tag: individual patient sample


title: 1115 (N) Hsac-02-74

description:
aRNA:	1115
Patient&sample ID:	AQ40
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	40
Histology:	0
Clinical history notes:
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.


title: 1068 (R) Hsac-02-71

description:
aRNA:	1068
Patient&sample ID:	AG243
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	243
Histology:	3A
Clinical history notes:	presented clinical signs of rejection, change of immunosuppresssion
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.


title: Rice Azucena 1ppm Arsenate Rep1

description: Gene expression data from rice roots (variety Azucena) grown in hydroponics for one week with 1ppm arsenate, rep1


title: Rice Azucena 0ppm Arsenate (Control) Rep1

description: Gene expression data from rice roots (variety Azucena) grown in hydroponics for one week with 0ppm arsenate, rep1

tag: Rice variety Azucena, 1 week in hydroponics, whole root system


title: astrocytes normoxia batch 3


title: HVSMC_Control_rep1

source_name: Human cerebral vascular smooth muscle cells (hcVSMCs) (passages 2-4) were obtained from human cerebral artery explants


title: 1152 (R) Hsac-02-75

description:
aRNA:	1152
Patient&sample ID:	AM14
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	14
Histology:	3A
Clinical history notes:	anti-rejection pulse 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.


title: 1077 (N) Hsac-02-73

description:
aRNA:	1077
Patient&sample ID:	AP10
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	10
Histology:	0
Clinical history notes:
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.


title: 1177 (N) Hsac-02-70

description:
aRNA:	1177
Patient&sample ID:	AJ18
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	18
Histology:	0
Clinical history notes:
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.


title: 1162 (R) Hsac-02-68

description:
aRNA:	1162
Patient&sample ID:	AM41
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	41
Histology:	3A
Clinical history notes:
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.


title: 1165 (R) Hsac-02-69

description:
aRNA:	1165
Patient&sample ID:	AN24
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	24
Histology:	3A
Clinical history notes:
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.


title: 1149 (N) Hsac-02-67

description:
aRNA:	1149
Patient&sample ID:	AR22
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	22
Histology:	0
Clinical history notes:
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.


title: 1079 (N) Hsac-02-65

description:
aRNA:	1079
Patient&sample ID:	AP17
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	17
Histology:	0
Clinical history notes:
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.


title: 1184 (N) Hsac-02-60

description:
aRNA:	1184
Patient&sample ID:	AL18
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	18
Histology:	0
Clinical history notes:
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.


title: 1171 (R) Hsac-02-58

description:
aRNA:	1171
Patient&sample ID:	AO6y
Sex:	female
Basic disease:	congenital cardiomyopathy
Days after Tx:	6y
Histology:	3B
Clinical history notes:	anti-rejection pulse 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.


title: 1159 (R) Hsac-02-56

description:
aRNA:	1159
Patient&sample ID:	AM26
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	26
Histology:	3A
Clinical history notes:
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.


title: 1119 (pre-R) Hsac-02-43

description:
aRNA	1119
Patient&sample ID:	AQ68
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	68
Histology:	0
Clinical history notes:	15 days pre-R; cutaneous Chagas disease reactivation
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.


title: 1140 (R) Hsac-02-66

description:
aRNA:	1140
Patient&sample ID:	AN14
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	14
Histology:	3A
Clinical history notes:
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.


title: 1110 (N) Hsac-02-42

description:
aRNA	1110
Patient&sample ID:	AQ26
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	26
Histology:	0
Clinical history notes:
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.


title: 1106 (N) Hsac-02-41

description:
aRNA	1106
Patient&sample ID:	AQ18
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	18
Histology:	0
Clinical history notes:
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.


title: 1077 (N) Hsac-02-35


title: 1119 (pre-R) Hsac-02-46

description:
aRNA:	1119
Patient&sample ID:	AQ68
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	68
Histology:	0
Clinical history notes:	15 days pre-R; cutaneous Chagas disease reactivation
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.


title: 1103 (N) Hsac-02-40

description:
aRNA	1103
Patient&sample ID:	AQ9
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	9
Histology:	0
Clinical history notes:
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.


title: 1168 (R) Hsac-02-57

description:
aRNA:	1168
Patient&sample ID:	AH8y
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	8y
Histology:	3A
Clinical history notes:	cardiac dysfunction
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.


title: 1156 (R) Hsac-02-32

description:
aRNA:	1156
Patient&sample ID:	AQ224
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	224
Histology:	3A
Clinical history notes:
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.


title: 4R4WB

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

hyb_protocol: Hybridization protocol was done according to chip manufacturers specifications (The Schnable Laboratory, Iowa State University)

scan_protocol: Arrays were scanned using an Affy428 scanner and Jaguar software.

data_processing: Raw signal intensities were log transformed and loess normalized using GeneMaths XT software (no background subtraction). The A-values (square root of the product of the log2 of the intensities for both channels) were calculated for each spot. Spots that had A-values of less than the average plus one standard deviation of the A-values of the empty spots were deleted from the data set.

organism: Zea mays

source_name: Weedy sample 4

label_protocol: Labeled cDNA was prepared from the 30 ug of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen) according to manufacture’s protocols.

growth_protocol: Plants were grown in field conditions with no supplemental water or fertilizer.

extract_protocol: The Pine Tree extraction procedure was used to extract RNA. Chang, S., J. Puryear, and J. Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.

treatment_protocol: Material was frozen in liquid N2 in the field at harvest.

tag: Maize (cultivar DKC46-22 planted at density of 7 plants/m2 in Aurora, SD on a Brandt silty clay loam soil) was grown to the 11-13 leaf stage in the presence of velvetleaf (Abutilon theophrasti) planted on the same day and thinned to density of ~4 weeds/m2. Field plots were fertilized with urea broadcast at 224 kg N ha-1 after planting. 3-4 inches of leaf blade from the tip of the top fully expanded leaf was collected from 4 plants in the plot and the material was pooled. Plant material was collected between 9-10am on July 11 2005 (after an evening thunderstorm).

source_name: Control sample 4

tag: Maize (cultivar DKC46-22 planted at density of 7 plants/m2 in Aurora, SD on a Brandt silty clay loam soil) was grown to the 12-14 leaf stage with broadleaf weed controlled by hand cultivation. Field plots were fertilized with urea broadcast at 224 kg N ha-1 after planting. 3-4 inches of leaf blade from the tip of the top fully expanded leaf was collected from 4 plants in the plot and the material was pooled. Plant material was collected between 9-10am on July 12 2005 (after an evening thunderstorm).


title: 4R1WB

source_name: Weedy sample 1

tag: Maize (cultivar DKC46-22 planted at density of 7 plants/m2 in Aurora, SD on a Brandt silty clay loam soil) was grown to the 11-13 leaf stage in the presence of velvetleaf (Abutilon theophrasti) planted on the same day and thinned to density of ~4 weeds/m2. Field plots were fertilized with urea broadcast at 224 kg N ha-1 after planting. 3-4 inches of leaf blade from the tip of the top fully expanded leaf was collected from 4 plants in the plot and the material was pooled. Plant material was collected between 2-3pm on July 11 2005 (just prior to a thunderstorm).


title: 2WR4B

source_name: Weedy sample 2


title: 1094 (N) Hsac-02-30

description:
aRNA:	1094
Patient&sample ID:	AI83
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	83
Histology:	0
Clinical history notes:
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.


title: 3R4WB

source_name: Control sample 3


title: 1137 (R) Hsac-02-28

description:
Array ID:	Hsac-02-28
aRNA:	1137
Patient&sample ID:	AN7
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	7
Histology (ISHLT grade):	3A
Clinical history notes:	anti-rejection pulse 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.


title: 3WR1B

source_name: Control sample 1

tag: Maize (cultivar DKC46-22 planted at density of 7 plants/m2 in Aurora, SD on a Brandt silty clay loam soil) was grown to the 12-14 leaf stage with broadleaf weed controlled by hand cultivation. Field plots were fertilized with urea broadcast at 224 kg N ha-1 after planting. 3-4 inches of leaf blade from the tip of the top fully expanded leaf was collected from 4 plants in the plot and the material was pooled. Plant material was collected between 2-3pm on July 11 2005 (just prior to a thunderstorm).

source_name: Weedy sample 3


title: 3WR4B


title: 1WR2B

source_name: Control sample 2


title: 1113 (N) Hsac-02-31

description:
aRNA:	1113
Patient&sample ID:	AK12
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	12
Histology:	0
Clinical history notes:
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.


title: 1068 (R) Hsac-02-29

description:
aRNA	1068
Patient&sample ID:	AG243
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	243
Histology:	3A
Clinical history notes:	presented clinical signs of rejection, change of immunosuppresssion
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.


title: 2R3WB


title: 1WR3B


title: HUVEC-rep4-LTD4+thrombin-1h

status: Public on Mar 14 2006

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

description: Cells stimulated for 1 hour with 100 nM LTD4 + 10 nM thrombin

data_processing: GCOS

label: Biotin/PE

source_name: HUVEC passage 1

tag: Confluent HUVEC passage 1,

tag: serum-free culture conditions,

tag: stimulation

value: 48 h after medium change


title: Rice Azucena 0ppm Arsenate (Control) Rep2

description: Gene expression data from rice roots (variety Azucena) grown in hydroponics for one week with 0ppm arsenate, rep2

source_name: Rice Hydroponic Roots 1 Week Old


title: HUVEC-rep1-thrombin-6h

description: Cells stimulated for 6 hours with 10 nM thrombin + 0.05% ethanol


title: HUVEC-rep1-control-6h

description: Cells stimulated for 6 hours with 0.05% ethanol


title: HUVEC-rep4-thrombin-1h

description: Cells stimulated for 1 hour with 10 nM thrombin + 0.05% ethanol


title: HUVEC-rep1-LTD4-6h

description: Cells stimulated for 6 hours with 100 nM LTD4


title: HUVEC-rep1-control-24h

description: Cells stimulated for 24 hours with 0.05% ethanol


title: HUVEC-rep1-LTD4-24h

description: Cells stimulated for 24 hours with 100 nM LTD4


title: HUVEC-rep3-LTD4+thrombin-1h


title: HUVEC-rep1-thrombin-24h

description: Cells stimulated for 24 hours with 10 nM thrombin + 0.05% ethanol


title: HUVEC-rep4-control-1h

description: Cells stimulated for 1 hour with 0.05% ethanol


title: HUVEC-rep4-LTD4-1h

description: Cells stimulated for 1 hour with 100 nM LTD4


title: HUVEC-rep3-thrombin-1h


title: HUVEC-rep3-LTD4-1h


title: HUVEC-rep2-LTD4+thrombin-1h


title: HUVEC-rep3-control-1h


title: HUVEC-rep2-thrombin-1h


title: nof_12h_202_19

status: Public on Mar 12 2006

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Neural stem/progenitor cells (NSPCs) were isolated from embryonic neocortex of timed-pregnant Sprague-Dawley rats (B&K, Sollentuna, Sweden) on embryonic day 14.5 (E14.5; E0.5 was defined as the day of copulatory plug) and cultured as described previously (1). Briefly, monolayer NSPC cultures were maintained in N2-medium with 10 ng/ml fibroblast growth factor 2 (FGF-2; Pepro Technologies, London, England) on tissue culture plastic, pre-coated with poly-L-ornithine (Sigma Chemical, St Louis, MO) and fibronectin (Invitrogen, Carlsbad, CA). Fresh FGF-2 was added daily and the medium changed every other day. When subconfluent, the cells were passaged using a cell scraper, re-plated and used for experiments 2-4 days thereafter. For differentiation experiments platelet-derived growth factor AA (PDGF-AA, Pepro Technologies, London, England) was added daily at a concentration of 10 ng/ml to stem cell cultures.Microarray hybridization and analysis were performed essentially as described (2). TotalRNA was isolated using the RNeasy kit (Qiagen, Valencia, CA). Total RNA (40 µg) from cells treated for a given period of time with PDGF-AA or control medium were labeled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 (Amersham).RNA isolated from FGF-treated cells was used as a reference and labeled with dCTP-Cy3. In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labeled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (Mver1.1.1, containing 15000 single stranded cDNA spots) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/ for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values = 2 for up-regulated genes and = 0.5 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Mver1.1.1 microarrays contain replicate spots corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Mver1.1.1_NCBI30).(1) Erlandsson A, Enarsson M, Forsberg-Nilsson K: Immature neurons from CNS stem cells proliferate in response to platelet-derived growth factor. J Neurosci 2001, 21(10):3483-3491.(2) Demoulin JB, Ericsson J, Kallin A, Rorsman C, Ronnstrand L, Heldin CH: Platelet-derived growth factor stimulates membrane lipid synthesis through activation of phosphatidylinositol 3-kinase and sterol regulatory element-binding proteins. J Biol Chem 2004, 279(34):35392-35402.

data_processing: GeneSpring 5.0

organism: Rattus norvegicus

source_name: Neural stem/progenitor cells (NSPCs), rat, FGF-2

extract_protocol: RNeasy Kit

tag: FGF2-treated cells

source_name: Neural stem/progenitor cells (NSPCs), rat, 12 hours, untreated

tag: 12 hours untreated stem cells


title: FE8 aza replicate 1

city: Berlin

first: Christine

last: Sers

address: Schumannstr. 20/21

department: Institute of Pathology

institute: Charite

description: FE8 HRAS-transformed rat fibroblast treated with 0.3uM 5-aza-deoxy-cytidine for 96h rep1

source_name: FE8 HRAS-transformed rat fibroblast

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was prepared from cultured cells using the TRIzol Reagent (Invitrogen) according to the manufacturer's instructions and dissolved in nuclease free water. After isolation, RNA used for microarray hybridisations was purified by the RNeasy Mini Kit (Qiagen) and the RNA quality was determined on a LabChip Bioanalyzer (Agilent Technologies).

tag: cultured cells


title: HUVEC-rep1-thrombin-1h


title: PDGF_12h_202_17

source_name: Neural stem/progenitor cells (NSPCs), rat, 12 hours, PDGFA

tag: 12 hours treated stem cells with PDGFA


title: noF_6d_202_10

source_name: Neural stem/progenitor cells (NSPCs), rat, 6 days, untreated

tag: 6 days untreated stem cells


title: noF_12h_202_13


title: PDGF_12h_202_16

tag: stem cells treated with PDGFA for 12 hours


title: FE8 aza replicate2

description: FE8 HRAS-transformed rat fibroblast treated with 0.3uM 5-aza-deoxy-cytidine for 96h rep2


title: HUVEC-rep1-control-1h


title: PDGF_6d_202_11

source_name: Neural stem/progenitor cells (NSPCs), rat, 6 days, PDGFA

tag: stem cells treated with PDGFA for 6 days


title: noF_12h_202_18


title: PDGF_12h_202_14


title: noF_6d_202_9


title: noF_12h_202_12


title: noF_6d_200_42


title: 208F aza replicate 2

description: 208F immortal fibroblasts treated with 0.3uM 5-aza-deoxy-cytidine for 96h rep2

source_name: 208Fimmortal rat fibroblast


title: 208F aza replicate 1

description: 208F immortal fibroblasts treated with 0.3uM 5-aza-deoxy-cytidine for 96h rep1


title: FE8 control

description: FE8 HRAS-transformed rat fibroblast untreated


title: PDGF_6D_186_34


title: noF_6d_202_7


title: PDGF_6D_186_32


title: 1128 (R) Hsac-02-51

description:
aRNA:	1128
Patient&sample ID:	AK74
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	74
Histology:	3A
Clinical history notes:
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.

source_name: reference pool

tag: pool of endomyocardial biopsies

source_name: endomyocardial biopsy


title: 208F control

description: 208F immortal fibroblasts untreated


title: PDGF_6d_184_41


title: Zorn_L1_Xenopus_laevis.txt

status: Public on Mar 11 2006

city: Cincinnati

first: Aaron

middle: M

last: Zorn

address: 3333 Burnet Ave

department: Develpomental Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Sample Number: 12
BioReplicate:  1
Experimental condition: control

hyb_protocol: 20 micrograms of labeled cRNA in a volume of 200 microliters was hybridized to the Affymetrix Xenopus Genecip in a standard Affymetrix Probe Array Cartridge at 45 degrees Celsius, using the fluidics protocol EukGE-WS2v4_450 of a Fluidics Station 450 (Affymetrix).

scan_protocol: The image file was captured on an Affymetrix GeneChip Scanner 3000 and initially processed with Genechip Operating Software 1v4 (Affymetrix).

data_processing:
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between 1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Each array was normalized the same. Global scaling is used adjusting the average intensity or signal value of each probe array to the same Target Intensity value (TGT) of 1500. Genechip Operating Software 1v4 (Affymetrix) was then used to generate CEL files from each experiment, which were then imported into GeneSpring for all further data analysis.
GeneSpring 7.1 software (Silicon Genetics) was used for data normalization, clustering and filtering.  Raw CEL file data from all the samples was pre-normalized using RMA (Robust Multichip Average). The average log intensity of the biological replicates was then normalized to the average log intensity of stage 11 whole embryo.

organism: Xenopus laevis

label_protocol: Quality of total RNA is verified by the Agilent Bioanalyzer 2100 (Hewelett Packard) using the RNA 6000 Nano Assay according to manufactures recommendations.  Then 10 micrograms of total RNA is used to make cDNA, from which botinylated cRNA probe was prepared using the standard Genechip Expression 3’ Amplification One-Cycle Target Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified on RNAeasy columns (Qiagen).  Ten micrograms of total RNA was used for cDNA syntheses and labeled RNA probe which was hybridized to Affymetrix Xenopus Genechips by the Cincinnati Children's Research Foundation microarray core facility, using the standard Affymetrix protocol.

treatment_protocol: Embryo manipulations and microinjections were preformed using standard procedures and embryos were staged according to the normal table of development for Xenopus laevis (Nieuwkoop and Faber, 1994). Two-cell stage embryos were vegetally injected with the following doses of antisense morpholino oligos or synthetic RNA: a combination of antisense morpholino oligos to Sox17a1 + Sox17a2 + Sox17b (20ng each) (Clements et al., 2003), Mixer antisense morpholino oligo (40ng) (Kofron et al., 2004), Cerberus-short RNA (1ng). For each biological sample for profiling, ~20 sibling embryos from a single mating or ~50 micro-dissected explants from sibling embryos were combined for individual RNA sample preparation.

tag: condition name

value: egg

tag: Developmental Stage

value: embryonic stage 1 egg


title: Zorn_B6_Xenopus_laevis.txt

description:
Sample Number:  18
BioReplicate:  2
Experimental condition: microdissected animal cap ectoderm at stage 9 and

value: animal cap

value: embryonic stage 11


title: Zorn_I_2A_Xenopus_laevis.txt

description:
Sample Number:  17
BioReplicate:  3
Experimental condition: microdissected animal cap ectoderm at stage 9 and


title: Zorn_f8b_Xenopus_laevis.txt

description:
Sample Number:  13
BioReplicate:  2
Experimental condition: control

value: control embryo 18

value: embryonic stage 18


title: Zorn_B2_Xenopus_laevis.txt

description:
Sample Number:  19
BioReplicate:  1
Experimental condition: microdissected animal cap ectoderm at stage 9 and


title: Zorn_f5b_Xenopus_laevis.txt

description:
Sample Number:  14
BioReplicate:  1
Experimental condition: control


title: Zorn_L2_Xenopus_laevis.txt

description:
Sample Number:  11
BioReplicate:  2
Experimental condition: control


title: Zorn_L3_Xenopus_laevis.txt

description:
Sample Number:  10
BioReplicate:  3
Experimental condition: control


title: Zorn_G_1B_Xenopus_laevis.txt

description:
Sample Number:  16
BioReplicate:  3
Experimental condition: control


title: Zorn_B5_Xenopus_laevis.txt

description:
Sample Number:  7
BioReplicate:  2
Experimental condition: control

value: control embryo 11


title: Zorn_D1_Xenopus_laevis.txt

description:
Sample Number:  5
BioReplicate:  4
Experimental condition: control


title: Zorn_H_2_Xenopus_laevis.txt

description:
Sample Number:  3
BioReplicate:  6
Experimental condition: control


title: Uninj_St_11_Xenopus_laevis.txt

description:
Sample Number:  9
BioReplicate:  8
Experimental condition: control


title: Zorn_C1_Xenopus_laevis.txt

description:
Sample Number:  6
BioReplicate:  3
Experimental condition: control


title: Zorn_J_1_Xenopus_laevis.txt

description:
Sample Number:  2
BioReplicate:  7
Experimental condition: control


title: Zorn_I_3B_Xenopus_laevis.txt

description:
Sample Number:  15
BioReplicate:  4
Experimental condition: control


title: Zorn_G_1A_Xenopus_laevis.txt

description:
Sample Number:  4
BioReplicate:  5
Experimental condition: control


title: Zorn_f3a_Xenopus_laevis.txt

description:
Sample Number:  29
BioReplicate:  2
Experimental condition: Sox17 depleted by antisense morpholino oligos


title: Zorn_B1_Xenopus_laevis.txt

description:
Sample Number:  8
BioReplicate:  1
Experimental condition: control


title: Zorn_C3_Xenopus_laevis.txt

description:
Sample Number:  31
BioReplicate:  1
Experimental condition: Sox17 depleted by antisense morpholino oligos


title: 32_ng_mixer_mo_1_Xeno#5E7C5.txt

description:
Sample Number:  28
BioReplicate:  1
Experimental condition: Mixer depleted by antisense morpholino oligos

value: Mixer-MO


title: Zorn_J_3_Xenopus_laevis.txt

description:
Sample Number:  27
BioReplicate:  2
Experimental condition: Mixer depleted by antisense morpholino oligos


title: Zorn_G_2A_Xenopus_laevis.txt

description:
Sample Number:  30
BioReplicate:  3
Experimental condition: Sox17 depleted by antisense morpholino oligos


title: HUVEC-rep1-LTD4-1h

description: Cells stimulated for 1 hour with 100 nM LTD4


title: Zorn_H_3_Xenopus_laevis.txt

description:
Sample Number:  20
BioReplicate:  2
Experimental condition: microdissected vegetal pole (endoderm) tissue

value: Vegetal endoderm


title: Zorn_K4_Xenopus_laevis.txt

description:
Sample Number:  22
BioReplicate:  2
Experimental condition: microdissected equatorial (mesendoderm) tissue

value: Equatorial


title: Zorn_H_4_Xenopus_laevis.txt

description:
Sample Number:  23
BioReplicate:  1
Experimental condition: microdissected equatorial (mesendoderm) tissue


title: MCE301 cells treated with SB for 0 h-2

status: Public on Mar 10 2006

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 0 h.

data_processing: GeneChip Analysis Suite

label: phycoerythrin

source_name: Mouse colonic epithelial cell line MCE301


title: MCE301 cells treated with SB for 12 h-2

description: A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 12 h.

tag: Mouse colonic epithelial cell line MCE301


title: MCE301 cells treated with SB for 12 h-1


title: Zorn_H_1_Xenopus_laevis.txt

description:
Sample Number:  25
BioReplicate:  3
Experimental condition: Nodal signaling blocked by injection of Cerb-S

value: Cerberus-Short


title: MCE301 cells treated with SB for 6 h-2

description: A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 6 h.


title: MCE301 cells treated with SB for 24 h-2

description: A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 24 h.


title: Zorn_B8_Xenopus_laevis.txt

description:
Sample Number:  21
BioReplicate:  1
Experimental condition: microdissected vegetal pole (endoderm) tissue


title: MCE301 cells treated with SB for 0 h-1


title: Transcriptional consequences of DNA gyrase inhibition (dnaC(Ts), 10min)

city: Saint Paul

first: Kyeong Soo

last: Jeong

state: MN

institute: University of Minnesota

description: Time course experiment (0, 5, 10, 15, 20 min)

data_processing: Lowess, Median normalization

organism: Escherichia coli

source_name: Norfloxacin treated E. coli dnaC(Ts) mutant for 10 min

tag: Strain

value: E coli MG1655, dnaC temperature-sensitive mutant (Tn10)

tag: Antibiotics

value: norfloxacin

tag: Dosage

value: 1ug/ml for 10 min after 90 min inhibition of initiation of DNA replication

tag: Medium

value: Minimal media (Vogel-Bonner) with 0.2% glucose

source_name: Nontreated E. coli dnaC(Ts) mutant at 0 min

value: no treatment after 90 min inhibition of initiation of DNA replication


title: Zorn_f4a_Xenopus_laevis.txt

description:
Sample Number:  24
BioReplicate:  2
Experimental condition: Nodal signaling blocked by injection of Cerb-S


title: Transcriptional consequences of DNA gyrase inhibition (dnaC(Ts), 20min)

source_name: Norfloxacin treated E. coli dnaC(Ts) mutant for 20min

value: 1ug/ml for 20 min after 90 min inhibition of initiation of DNA replication


title: Transcriptional consequences of DNA gyrase inhibition (dnaC(Ts), 15min)

source_name: Norfloxacin treated E. coli dnaC(Ts) mutant for 15min

value: 1ug/ml for 15 min after 90 min inhibition of initiation of DNA replication


title: isoflurane 05

city: Stony Brook

first: Achim

last: Bell

address: 101 Nicolls Road

department: Anesthesiology

institute: SUNY Stony Brook

description: Fear conditioning in rats leads to long term memory (LTM) formation. A central substrate for this type of LTM is the basolateral amygdala. We sought the expression changes specific to LTM at 6h following pain (a component of conditioning), following anesthesia with isoflurane (a general anesthetic and an effective amnestic agent), and following conditioning during isoflurane. For this also see GSE1779.

data_processing: raw data from Affymetrix

label: fluorscent label via ENZO BioArray RNA Transcript Labeling Kit

source_name: basolateral amygdala


title: PDGF_12h_202_15

description:
Neural stem/progenitor cells (NSPCs) were isolated from embryonic neocortex of timed-pregnant Sprague-Dawley rats (B&K, Sollentuna, Sweden) on embryonic day 14.5 (E14.5; E0.5 was defined as the day of copulatory plug) and cultured as described previously (1). Briefly, monolayer NSPC cultures were maintained in N2-medium with 10 ng/ml fibroblast growth factor 2 (FGF-2; Pepro Technologies, London, England) on tissue culture plastic, pre-coated with poly-L-ornithine (Sigma Chemical, St Louis, MO) and fibronectin (Invitrogen, Carlsbad, CA). Fresh FGF-2 was added daily and the medium changed every other day. When subconfluent, the cells were passaged using a cell scraper, re-plated and used for experiments 2-4 days thereafter. For differentiation experiments platelet-derived growth factor AA (PDGF-AA, Pepro Technologies, London, England) was added daily at a concentration of 10 ng/ml to stem cell cultures.Microarray hybridization and analysis were performed essentially as described (2). TotalRNA was isolated using the RNeasy kit (Qiagen, Valencia, CA). Total RNA (40 µg) from cells treated for a given period of time with PDGF-AA or control medium were labeled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 (Amersham).RNA isolated from FGF-treated cells was used as a reference and labeled with dCTP-Cy3. In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labeled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (Mver1.1.1, containing 15000 single stranded cDNA spots) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/ for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values = 2 for up-regulated genes and = 0.5 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Mver1.1.1 microarrays contain replicate spots corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Mver1.1.1_NCBI30).(1) Erlandsson A, Enarsson M, Forsberg-Nilsson K: Immature neurons from CNS stem cells proliferate in response to platelet-derived growth factor. J Neurosci 2001, 21(10):3483-3491.(2) Demoulin JB, Ericsson J, Kallin A, Rorsman C, Ronnstrand L, Heldin CH: Platelet-derived growth factor stimulates membrane lipid synthesis through activation of phosphatidylinositol 3-kinase and sterol regulatory element-binding proteins. J Biol Chem 2004, 279(34):35392-35402.
Neural stem/progenitor cells (NSPCs) were isolated from embryonic neocortex of timed-pregnant Sprague-Dawley rats (B&K, Sollentuna, Sweden) on embryonic day 14.5 (E14.5; E0.5 was defined as the day of copulatory plug) and cultured as described previously (1). Briefly, monolayer NSPC cultures were maintained in N2-medium with 10 ng/ml fibroblast growth factor 2 (FGF-2; Pepro Technologies, London, England) on tissue culture plastic, pre-coated with poly-L-ornithine (Sigma Chemical, St Louis, MO) and fibronectin (Invitrogen, Carlsbad, CA). Fresh FGF-2 was added daily and the medium changed every other day. When subconfluent, the cells were passaged using a cell scraper, re-plated and used for experiments 2-4 days thereafter. For differentiation experiments platelet-derived growth factor AA (PDGF-AA, Pepro Technologies, London, England) was added daily at a concentration of 10 ng/ml to stem cell cultures.Microarray hybridization and analysis were performed essentially as described (2). TotalRNA was isolated using the RNeasy kit (Qiagen, Valencia, CA). Total RNA (40 µg) from cells treated for a given period of time with PDGF-AA or control medium were labeled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 (Amersham).RNA isolated from FGF-treated cells was used as a reference and labeled with dCTP-Cy3. In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labeled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (Mver1.1.1, containing 15000 single stranded cDNA spots) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/ for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values = 2 for up-regulated genes and = 0.5 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Mver1.1.1 microarrays contain replicate spots corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Mver1.1.1_NCBI30).(1) Erlandsson A, Enarsson M, Forsberg-Nilsson K: Immature neurons from CNS stem cells proliferate in response to platelet-derived growth factor. J Neurosci 2001, 21(10):3483-3491.(2) Demoulin JB, Ericsson J, Kallin A, Rorsman C, Ronnstrand L, Heldin CH: Platelet-derived growth factor stimulates membrane lipid synthesis through activation of phosphatidylinositol 3-kinase and sterol regulatory element-binding proteins. J Biol Chem 2004, 279(34):35392-35402.


title: isoflurane 01


title: Zorn_D2_Xenopus_laevis.txt

description:
Sample Number:  26
BioReplicate:  1
Experimental condition: Nodal signaling blocked by injection of Cerb-S


title: MCE301 cells treated with SB for 24 h-1


title: LmajF-pro (22665)

city: West Lafayette

first: Timothy

middle: R

last: Holzer

state: IN

address: 175 S. University St.

department: Biochemistry

institute: Purdue University

description: For the peer-reviewed publication describing this sample, refer to: Timothy R. Holzer, W.R. McMaster, and James D. Forney. Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana. Mol Biochem Parasitol. 146(2): 198-218 (2006).

hyb_protocol: Refer to: E.F. Nuwaysir, W. Huang and T.J. Albert et al., Gene expression analysis using oligonucleotide arrays produced by maskless photolithography, Genome Res 12 (2002), pp. 1749–1755.

data_processing: Data were scaled by trimmed mean (set to 10%) using one replicate Lmex-pro array as a baseline (Lmex-pro 22359, GSM98805). This process assumes that the majority of the genes on the array do not differ significantly in their individual expression intensities among samples, and thus the mean value all of gene intensities on the array theoretically should have the same value. This data transformation protocol has been described in detail previously in D. Kaushal and C.W. Naeve, Loading and preparing data for analysis in spotfire. In: A.D. Baxevanis, Editor, Current protocols in bioinformatics, Wiley, New York (2004) [Unit 7.8].

organism: Leishmania major

source_name: Leishmania major promastigote

growth_protocol: Promastigotes of  L. major Friedlin were cultured in M199 medium containing 5% (v/v) fetal bovine serum, 5% (v/v) bovine embryonic fluid at 26 °C as described previously for Leishmania (J.H. LeBowitz, Transfection experiments with Leishmania, Methods Cell Biol 45 (1994), pp. 65–78.). Cultures were maintained by serial dilutions 1:100, every 3–4 days.

extract_protocol: Logarithmic phase cultures (5 × 10^6 to 9 × 10^6 cells/ml) were used to isolate RNA from axenic cultures. Cells were counted on a hemacytometer. Qiagen RNeasy columns were used to isolate total RNA according to the manufacturer's instructions. RNA was analyzed on a denaturing agarose gel to check for degradation. The OD260:280 for each sample was greater than 2.1. Total RNA samples were tested for purity and integrity by NimbleGen Systems, Inc. (Madison, WI) using an RNA LabChip on an Agilent 2100 Bioanalyzer before labeling.

tag: WHO strain MHOM/IL/80/Friedlin

tag: Logarithmic phase axenic Leishmania major promastigotes


title: isoflurane 02


title: isoflurane 03


title: isoflurane 04


title: Lmex-axenic-ama (22663)

scan_protocol: Refer to: E.F. Nuwaysir, W. Huang and T.J. Albert et al., Gene expression analysis using oligonucleotide arrays produced by maskless photolithography, Genome Res 12 (2002), pp. 1749–1755.

organism: Leishmania mexicana

source_name: Leishmania mexicana amastigote, axenic

growth_protocol: Axenic amastigotes of L. mexicana were obtained by shifting the incubation conditions of a saturated culture of L. mexicana promastigotes from 26 to 33 °C and pH 5.5 in a modified UM 54 medium as described previously (L.L. Moore, C. Santrich and J.H. LeBowitz, Stage-specific expression of the Leishmania mexicana paraflagellar rod protein PFR-2, Mol Biochem Parasitol 80 (1996), pp. 125–135.). Amastigote cells were visualized under the light microscope to confirm transformation. Cultures were maintained by serial dilutions 1:25, every 3–4 days.

tag: WHO strain MNYC/BZ/62/m379

tag: Leishmania mexicana amastigote, axenic


title: Lmex-axenic-ama (22607)

label_protocol: Refer to: E.F. Nuwaysir, W. Huang and T.J. Albert et al., Gene expression analysis using oligonucleotide arrays produced by maskless photolithography, Genome Res 12 (2002), pp. 1749–1755.


title: Transcriptional consequences of DNA gyrase inhibition (topA-, 15min)

source_name: Norfloxacin treated E. coli topA- mutant for 15 min

value: E coli MG1655, topA deletion mutant(Chloramphenicol replacement)

value: 1ug/ml for 15 min

source_name: Nontreated E. coli topA- mutant at 0 min

value: E coli MG1655 topA deletion mutant (Chloramphenicol replacement)

value: no treatment

tag: Reference channel


title: Transcriptional consequences of DNA gyrase inhibition (topA-, 10min)

source_name: Norfloxacin treated E. coli topA- mutant for 10 min

value: 1ug/ml for 5 min


title: Transcriptional consequences of DNA gyrase inhibition (topA-, 20min)

source_name: Norfloxacin treated E. coli topA- mutant for 20 min

value: 1ug/ml for 20 min


title: Transcriptional consequences of DNA gyrase inhibition (dnaC(Ts), 5min)

source_name: Norfloxacin treated E. coli dnaC(Ts) mutant for 5min

value: 1ug/ml for 5 min after 90 min inhibition of initiation of DNA replication


title: Transcriptional consequences of DNA gyrase inhibition (topA-, 5min)

source_name: Norfloxacin treated E. coli topA- mutant for 5 min


title: MCE301 cells treated with SB for 6 h-1


title: LmajF-pro (22687)


title: Transcriptional consequences of DNA gyrase inhibition (recA-, 20min)

source_name: Norfloxacin treated E. coli recA- mutant for 20 min

value: E coli MG1655, recA deletion mutant(KAN replacement)

source_name: Nontreated E. coli recA- mutant at 0 min

value: E coli MG1655 recA deletion mutant (Kan replacement)


title: Transcriptional consequences of DNA gyrase inhibition (Wild type 10 min treat)

source_name: Norfloxacin treated E. coli for 10 min

value: E coli MG1655

value: 1ug/ml for 10 min

source_name: Nontreated E. coli at 0 min


title: Transcriptional consequences of DNA gyrase inhibition (recA-, 10min)

source_name: Norfloxacin treated E. coli recA- mutant for 10 min

value: norfloxacin


title: Transcriptional consequences of DNA gyrase inhibition (wild type, 20min treatment)

source_name: Norfloxacin treated E. coli for 20 min


title: Transcriptional consequences of DNA gyrase inhibition (wild type, 15 min treat)

source_name: Norfloxacin treated E. coli for 15 min


title: Transcriptional consequences of DNA gyrase inhibition (recA-, 15min)

source_name: Norfloxacin treated E. coli recA- mutant for 15 min


title: Transcriptional consequences of DNA gyrase inhibition (wild type, 5min)

source_name: Norfloxacin treated E. coli for 5 min


title: Lmex-lesion-ama (28993)

source_name: Leishmania mexicana amastigote, lesion-derived

growth_protocol: L. mexicana lesion amastigotes were obtained by infecting BALB/c mice subcutaneously in the flank with 1 x 10^5 late stationary-phase promastigotes. Lesions developed 6 to 8 weeks after infection.

extract_protocol: esion amastigotes were purified essentially as described previously substituting the Dounce homogenizer step by the rupturing of the infected macrophages by syringing through a 26 gauge needle 20 times, and excluding the ammonium chloride and polycarbonate filter steps (T.A. Glaser, S.J. Wells, T.W. Spithill, J.M. Pettitt, D.C. Humphris and A.J. Mukkada, Leishmania major and L. donovani: a method for rapid purification of amastigotes, Exp Parasitol 71 (1990), pp. 343–345.)


title: Lmex-lesion-ama (26020)

extract_protocol: Lesion amastigotes were purified essentially as described previously substituting the Dounce homogenizer step by the rupturing of the infected macrophages by syringing through a 26 gauge needle 20 times, and excluding the ammonium chloride and polycarbonate filter steps (T.A. Glaser, S.J. Wells, T.W. Spithill, J.M. Pettitt, D.C. Humphris and A.J. Mukkada, Leishmania major and L. donovani: a method for rapid purification of amastigotes, Exp Parasitol 71 (1990), pp. 343–345.)


title: Lmex-pro (22407)

source_name: Leishmania mexicana Promastigote

growth_protocol: Promastigotes of L. mexicana were cultured in M199 medium containing 5% (v/v) fetal bovine serum, 5% (v/v) bovine embryonic fluid at 26 °C as described previously for Leishmania (J.H. LeBowitz, Transfection experiments with Leishmania, Methods Cell Biol 45 (1994), pp. 65–78.). Cultures were maintained by serial dilutions 1:100, every 3–4 days.

tag: Logarithmic phase axenic promastigote culture


title: WT-SOD1 mouse spinal cord 110 day

status: Public on Mar 09 2006

city: Chicago

first: Thomas

middle: J

last: Lukas

state: IL

address: 303 E. Chicago Ave

department: MPBC

institute: Northwestern University

description: Each array hybridization and scan was performed once.

hyb_protocol: 15 micrograms of cRNA were added to 300 microliters of hybridization buffer containing 0.1 mg/mL of herring sperm DNA, 0.5 mg/mL acetylated bovine serum albumin, and MES hybridization buffer (Sigma). Standard Affymetrix controls were added and 200 microliters of this mixture hybridized to the chip (MG-U74v2A) for 16 hr. Probe arrays were washed and stained in an Affymetrix Fluidics station using preprogrammed methods.  The arrays were then stained with streptavidin phycoerythrin and the signal amplified with biotinylated antibody

scan_protocol: Probe arrays were then scanned in the Affymetrix GeneChip scanner.

data_processing: Affymetrix MicroDB - .cel file - BRB array tools

label: Biotin

molecule: polyA RNA

source_name: WT-SOD1 transgenic mouse

label_protocol: First strand synthesis was done using Superscipt choice system kit (Life technologies). A T7(N)24 primer was used starting with 1 microgram of polyA RNA and 400 units of Superscript II reverse transcriptase.  Second strand synthesis was done with DNA ligase/DNA polymerase mix and RNAase H in the two step reaction following the manufacturer's instructions. cDNA was purified by phenol-chloroform extraction and ethanol precipitation. In vitro transcription and biotin labeling of the purified cDNA was performed using the Affymetrix IVT kit.  cRNA was purified using an RNeasy spin column (Qiagen) followed by ethanol preciptitation. Twenty micrograms of cRNA was fragmented accoriding to the kit instructions.

extract_protocol: Total RNA from mouse spinal cords (4)was prepared with the Trizol method (Invitrogen 15596-018).  PolyA RNA was isolated using an Oligotex mRNA kit.

tag: Strain:B6SJL-WT-SOD1 transgenic mouse

tag: Age

value: 110 days


title: WT-SOD1 mouse spinal cord 75 day

source_name: WT-SOD1 transgenic

value: B6SJL-WT-SOD1 transgenic mouse

value: 75 days


title: Lmex-pro (22409)

growth_protocol: Promastigotes of L. mexicana were cultured in M199 medium containing 5% (v/v) fetal bovine serum, 5% (v/v) bovine embryonic fluid at 26 °C as described previously (J.H. LeBowitz, Transfection experiments with Leishmania, Methods Cell Biol 45 (1994), pp. 65–78.). Cultures were maintained by serial dilutions 1:100, every 3–4 days.


title: G93A-SOD1 mouse spinal cord 75 day

source_name: G93A-SOD1 mouse

value: 75 day


title: G93A-SOD1 mouse spinal cord 110 day


title: Lmex-lesion-ama (29076)

tag: Leishmania mexicana amastigote, lesion-derived


title: NM Spinal cord 110 day

source_name: Normal mouse


title: Lmex-pro (22359)

hyb_protocol: Refer to: E.F. Nuwaysir, W. Huang and T.J. Albert et al., Gene expression analysis using oligonucleotide arrays produced by maskless photolithography, Genome Res 12 (2002), pp. 1749–1755


title: NM Spinal cord 75 day


title: Zorn_f5a_Xenopus_laevis.txt

description:
Sample Number:  1
BioReplicate:  9
Experimental condition: control

value: control embryo 11

value: embryonic stage 11


title: Lmex-axenic-ama (22411)

source_name: Leishmania mexicana amastigote, axenic


title: Human Prostate epithelial cells LNCaP

city: Roma

first: Antonella

last: Farsetti

address: Via delle Messi d'Oro 156

department: Centro Ricerca Sperimentale

country: Italy

institute: Istituto Regina Elena

description: According to Affymetrix Gene expression Analysis Technical manual REV.3

label: SAPE

source_name: ATCC company

label_protocol: according to Affymetrix protocol

tag: Human prostate epithelial cells from metastatic site

value: left supraclavicular lymph node


title: P32 Fetal Normal Male placenta

city: Stanford

first: Ruchira

last: Sood

state: CA

address: 3373 Hillview avenue Room 220

department: Pathology

institute: Stanford University

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19217.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: PR (Placenta + CRG)

tag: PR (Placenta + CRG)

source_name: P32 Fetal Normal Male placenta

tag: P32 Fetal Normal Male placenta


title: Transcriptional consequences of DNA gyrase inhibition (recA-, 5min)

source_name: Norfloxacin treated E. coli recA- mutant for 5 min

value: Minimal media (Vogel-Bonner) with 0.2% glucose

source_name: Nontreated E. coli recA- mutant at 0 min


title: Human Prostate epithelial cells PrEC

source_name: Cambrex company

tag: Human prostate epithelial cells with basaloid phenotype


title: Human Prostate epithelial cells PrEC 3p


title: P32 Amnion Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19218.gif; format: GIF

source_name: P32 Amnion Normal Male placenta

tag: P32 Amnion Normal Male placenta


title: Human Prostate epithelial cells PrEC 4p


title: Human prostate hyperplasia primary culture C17

source_name: Human Benign Prostatic Hyperplasia (BPH) tissue

tag: Epithelial prostate primary cells from fresh explant of benign hyperplasia


title: P23 Fetal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21859.gif; format: GIF

source_name: P23 Fetal Normal Female placenta

tag: P23 Fetal Normal Female placenta


title: P32 Maternal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19216.gif; format: GIF

source_name: P32 Maternal Normal Male placenta

tag: P32 Maternal Normal Male placenta


title: P32 Middle Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20063.gif; format: GIF

source_name: P32 Middle Normal Male placenta

tag: P32 Middle Normal Male placenta


title: P47 Chorion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23078.gif; format: GIF

source_name: P47 Chorion Normal male placenta

tag: P47 Chorion Normal male placenta


title: Human normal prostate primary culture N1

source_name: Human normal prostate tissue

tag: Epithelial prostate primary cells from fresh explant from normal tissue, obtained from a cystoprostatectomy of a patient with a bladder carcinoma with no lesions in the prostate


title: Human normal prostate primary culture C16sx

tag: Epithelial prostate primary cells from fresh explant of controlateral normal tissue characterized by the presence of few areas of "PIN" (Prostatic In Situ Neoplasia)


title: P32 Chorion Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19221.gif; format: GIF

source_name: P32 Chorion Normal Male placenta

tag: P32 Chorion Normal Male placenta


title: P34 Chorion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19222.gif; format: GIF

source_name: P34 Amnion/Chorion Normal Female placenta


title: P47 Maternal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23085.gif; format: GIF

source_name: P47 Maternal Normal male placenta

tag: P47 Maternal Normal male placenta


title: P23 Amnion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21852.gif; format: GIF

source_name: P23 Amnion Normal Female placenta

tag: P23 Amnion Normal Female placenta


title: P47 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23081.gif; format: GIF

source_name: P47 Fetal Normal male placenta

tag: P47 Fetal Normal male placenta


title: P23 Chorion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21855.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P23 Chorion Normal Female placenta

tag: P23 Chorion Normal Female placenta


title: Human prostate hyperplasia primary culture C10


title: P23 Maternal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21849.gif; format: GIF

source_name: P23 Maternal Normal Female placenta

tag: P23 Maternal Normal Female placenta


title: P34 Cord Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19223.gif; format: GIF

tag: PR (Placenta + CRG)

source_name: P34 Cord Normal Female placenta

tag: P34 Cord Normal Female placenta


title: Human prostate cancer primary culture C45

source_name: Human prostate cancer tissue

tag: Epithelial prostate primary cells from fresh tumor explant


title: P34 Fetal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19224.gif; format: GIF

source_name: P34 Fetal Normal Female placenta

tag: P34 Fetal Normal Female placenta


title: P32 Cord Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19220.gif; format: GIF

source_name: P32 Cord Normal Male placenta

tag: P32 Cord Normal Male placenta


title: Human prostate cancer primary culture C43dx

description: According to Affymetrix Gene expression Analysis Technical manual REV.3


title: P22 Chorion Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21841.gif; format: GIF

source_name: P22 Chorion Normal Male placenta

tag: P22 Chorion Normal Male placenta


title: P22 Maternal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21840.gif; format: GIF

source_name: P22 Maternal Normal Male placenta

tag: P22 Maternal Normal Male placenta


title: P23 Middle Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21846.gif; format: GIF

source_name: P23 Middle Normal Female placenta

tag: P23 Middle Normal Female placenta


title: Human prostate cancer primary culture C41sx


title: Human prostate cancer primary culture C39sx


title: P22 Fetal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21843.gif; format: GIF

source_name: P22 Fetal Normal Male placenta

tag: P22 Fetal Normal Male placenta


title: P24 Maternal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21870.gif; format: GIF

source_name: P24 Maternal Normal Female placenta

tag: P24 Maternal Normal Female placenta


title: P24 Fetal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21872.gif; format: GIF

source_name: P24 Fetal Normal Female placenta

tag: P24 Fetal Normal Female placenta


title: P24 Chorion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21874.gif; format: GIF

source_name: P24 Chorion Normal Female placenta

tag: P24 Chorion Normal Female placenta


title: P24 Middle Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21863.gif; format: GIF

source_name: P24 Middle Normal Female placenta

tag: P24 Middle Normal Female placenta


title: Human prostate cancer primary culture C40dx


title: P22 Middle Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/21839.gif; format: GIF

source_name: P22 Middle Normal Male placenta

tag: P22 Middle Normal Male placenta


title: P18 Maternal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35637.gif; format: GIF

source_name: P18 Maternal Normal Male placenta

tag: P18 Maternal Normal Male placenta


title: P47 Middle Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23088.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P47 Middle Normal male placenta

tag: P47 Middle Normal male placenta


title: P34 Maternal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18347.gif; format: GIF

source_name: P34 Maternal Normal Female placenta 0.5 hr


title: Human prostate cancer primary culture C35sx


title: P34 Middle Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19225.gif; format: GIF

source_name: P34 Middle Normal Female placenta

tag: P34 Middle Normal Female placenta


title: Human prostate cancer primary culture C39dx

source_name: Human prostate cancer tissue


title: P15 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18127.gif; format: GIF

tag: PR (Placenta + CRG)

source_name: P15 Fetal Normal male placenta

tag: P15 Fetal Normal male placenta


title: Human prostate cancer primary culture C38dx

tag: Epithelial prostate primary cells from fresh tumor explant


title: P17 Maternal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35635.gif; format: GIF

source_name: P17 Maternal Normal Male placenta

tag: P17 Maternal Normal Male placenta


title: Human prostate cancer primary culture C29dx


title: P17 Chorion Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35634.gif; format: GIF

source_name: P17 Chorion Normal Male placenta

tag: P17 Chorion Normal Male placenta


title: P20 Middle Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35658.gif; format: GIF

source_name: P20 Middle Normal male placenta

tag: P20 Middle Normal male placenta


title: P25 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35656.gif; format: GIF

source_name: P25 Fetal Normal male placenta

tag: P25 Fetal Normal male placenta


title: P20 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35646.gif; format: GIF

source_name: P20 Fetal Normal male placenta

tag: P20 Fetal Normal male placenta


title: P20 Maternal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35644.gif; format: GIF

source_name: P20 Maternal Normal male placenta

tag: P20 Maternal Normal male placenta


title: Human prostate cancer primary culture C28dx

description: According to Affymetrix Gene expression Analysis Technical manual REV.3


title: P84 Fetal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34212.gif; format: GIF

source_name: P84 Fetal Normal Female placenta

tag: P84 Fetal Normal Female placenta


title: P15 Cord Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18125.gif; format: GIF

source_name: P15 Cord Normal male placenta

tag: P15 Cord Normal male placenta


title: P20 Chorion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35648.gif; format: GIF

source_name: P20 Chorion Normal male placenta

tag: P20 Chorion Normal male placenta


title: Human prostate cancer primary culture C25dx

source_name: Human prostate tumor tissue


title: Human prostate cancer primary culture C27dx


title: P72 Chorion Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34206.gif; format: GIF

source_name: P72 Chorion Normal Male placenta

tag: P72 Chorion Normal Male placenta


title: P15 Chorion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18122.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P15 Chorion Normal male placenta

tag: P15 Chorion Normal male placenta


title: P28 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35678.gif; format: GIF

source_name: P28 Fetal Normal male placenta

tag: P28 Fetal Normal male placenta


title: Human prostate cancer primary culture C24sx


title: P21 Fetal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18152.gif; format: GIF

source_name: P21 Fetal Normal Female placenta

tag: P21 Fetal Normal Female placenta


title: P21 Chorion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18147.gif; format: GIF

source_name: P21 Chorion Normal Female placenta

tag: P21 Chorion Normal Female placenta


title: P18 Middle Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35640.gif; format: GIF

tag: PR (Placenta + CRG)

source_name: P18 Middle Normal Male placenta

tag: P18 Middle Normal Male placenta


title: P21 Maternal Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18150.gif; format: GIF

source_name: P21 Maternal Normal Female placenta

tag: P21 Maternal Normal Female placenta


title: P84 Chorion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34210.gif; format: GIF

source_name: P84 Chorion Normal Female placenta

tag: P84 Chorion Normal Female placenta


title: Human prostate cancer primary culture C19sx

source_name: Human prostate cancer tissue

tag: Epithelial prostate primary cells from fresh tumor explant


title: Human prostate cancer primary culture C22dx


title: P72 Amnion Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34205.gif; format: GIF

source_name: P72 Amnion Normal Male placenta

tag: P72 Amnion Normal Male placenta


title: P28 Middle Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35676.gif; format: GIF

source_name: P28 Middle Normal male placenta

tag: P28 Middle Normal male placenta


title: P84 Amnion Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34208.gif; format: GIF

source_name: P84 Amnion Normal Female placenta

tag: P84 Amnion Normal Female placenta


title: P28 Chorion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35672.gif; format: GIF

source_name: P28 Chorion Normal male placenta

tag: P28 Chorion Normal male placenta


title: P15 Amnion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18120.gif; format: GIF

source_name: P15 Amnion Normal male placenta

tag: P15 Amnion Normal male placenta


title: P18 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35642.gif; format: GIF

source_name: P18 Fetal Normal male placenta

tag: P18 Fetal Normal male placenta


title: P21 Middle Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18153.gif; format: GIF

source_name: P21 Middle Normal Female placenta

tag: P21 Middle Normal Female placenta


title: Human prostate cancer primary culture C19dx

description: According to Affymetrix Gene expression Analysis Technical manual REV.3

source_name: Human prostate tumor tissue


title: P5 Maternal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18133.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P5 Maternal Normal male placenta

tag: P5 Maternal Normal male placenta


title: Human prostate cancer primary culture C14sx


title: P27 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35669.gif; format: GIF

source_name: P27 Fetal Normal male placenta

tag: P27 Fetal Normal male placenta


title: P21 Cord Normal Female placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18143.gif; format: GIF

source_name: P21 Cord Normal Female placenta

tag: P21 Cord Normal Female placenta


title: P17 Fetal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35639.gif; format: GIF

source_name: P17 Fetal Normal Male placenta

tag: P17 Fetal Normal Male placenta


title: MCF7 E2F1 ChIP_array 40016

type: genomic

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: determination of E2F1 binding sites in MCF7 cells; note hg17 array

data_processing: by NimbleGen

molecule: genomic DNA

source_name: E2F1 ChIP

source_name: matched Total DNA


title: Human prostate cancer primary culture C13dx


title: Ecoli_Temperature upshift in gyrBT mutant T3

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: Temperature upshift to 42 C in gyrBT mutant, 10 min vs before upshift

data_processing: Normalized log (2) ratio of Cy5/Cy3, normalized using lowess

source_name: Escherichia coli W3110gyrb234, LB

tag: Escherichia coli W3110gyrb234, LB

source_name: Escherichia coli W3110gyrb234, LB, 10 min after upshift to 42 C

tag: Escherichia coli W3110gyrb234, LB, 2 min after upshift to 42 C


title: Human prostate cancer primary culture C11sx

source_name: Human prostate cancer tissue


title: Ecoli_Temperature upshift in gyrBT mutant T2

description: Temperature upshift to 42 C in gyrBT mutant, 5 min vs before upshift

source_name: Escherichia coli W3110gyrb234, LB, 5 min after upshift to 42 C


title: P20 Cord Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35638.gif; format: GIF

tag: PR (Placenta + CRG)

source_name: P20 Cord Normal Male placenta

tag: P20 Cord Normal Male placenta


title: HeLa MYC ChIP_array 58908

description: Determination of binding sites of MYC in HeLa cells using ChIP-chip, hg17 NimbleGen array

data_processing: minimal by NimbleGen

source_name: MYC ChIP

tag: ChIP


title: P31 Chorion normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23096.gif; format: GIF

source_name: P31 Chorion normal male placenta

tag: P31 Chorion normal male placenta


title: Human prostate cancer primary culture C3dx

tag: Epithelial prostate primary cells from fresh tumor explant


title: P30 Amnion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23087.gif; format: GIF

source_name: P30 Amnion Normal male placenta

tag: P30 Amnion Normal male placenta


title: P5 Middle Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18135.gif; format: GIF

source_name: P5 Middle Normal male placenta

tag: P5 Middle Normal male placenta


title: HeLa MYC ChIP_array 46679

source_name: MYC ChIP HeLa cells

tag: Chip


title: HeLa MYC ChIP_array 58905

tag: HeLa cells

tag: Total


title: P27 Chorion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35663.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P27 Chorion Normal male placenta

tag: P27 Chorion Normal male placenta


title: Human prostate cancer primary culture  sample C2dx


title: Ecoli_Stationary phase in LB T6

status: Public on Mar 08 2006

type: mixed

description:
Stationary phase in LB, OD 3.1 for 60 min

Ecoli MG1655, stationary phase in LB vs genomic DNA

source_name: Escherichia coli MG1655 genomic DNA

label_protocol: Labeling of DNA using DNA polymerase (Klenow fragment)

tag: Escherichia coli MG1655 genomic DNA

source_name: Escherichia coli MG1655,  stationary phase in LB, OD 3.1 for 60 min


title: Ecoli_Temperature upshift in gyrBT mutant T1

description: Temperature upshift to 42 C in gyrBT mutant, 2 min vs before upshift

source_name: Escherichia coli W3110gyrb234, LB, 2 min after upshift to 42 C


title: P30 Chorion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23090.gif; format: GIF

source_name: P30 Chorion Normal male placenta

tag: P30 Chorion Normal male placenta


title: Ecoli_Stationary phase in LB T5

description:
Stationary phase in LB, OD 3.1 for 40 min

Ecoli MG1655, stationary phase in LB vs genomic DNA

source_name: Escherichia coli MG1655,  Stationary phase in LB OD 3.1 for 40 min


title: Ecoli_Stationary phase in LB T4

description:
Stationary phase in LB, OD 3.1 for 20 min

Ecoli MG1655, stationary phase in LB vs genomic DNA

source_name: Escherichia coli MG1655, Stationary phase in LB OD 3.1 for 20 min


title: P30 Maternal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23114.gif; format: GIF

source_name: P30 Maternal Normal male placenta

tag: P30 Maternal Normal male placenta


title: P25 Middle Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35660.gif; format: GIF

source_name: P25 Middle Normal male placenta

tag: P25 Middle Normal male placenta


title: IgG control experiment in HeLa

description: Control Experiment

data_processing: minimal, see NimbleGen website

source_name: IgG ChIP

source_name: Matched Total DNA


title: P30 Middle Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23117.gif; format: GIF

source_name: P30 Middle Normal male placenta

tag: P30 Middle Normal male placenta


title: Human prostate cancer primary culture C1dx

description: According to Affymetrix Gene expression Analysis Technical manual REV.3

source_name: Human prostate tumor

tag: Epithelial prostate primary cells from fresh tumor explant.


title: P72 Maternal Normal Male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34207.gif; format: GIF

tag: PR (Placenta + CRG)

source_name: P72 Maternal Normal Male placenta

tag: P72 Maternal Normal Male placenta


title: P31 Fetal normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23099.gif; format: GIF

source_name: P31 Fetal normal  male placenta

tag: P31 Fetal normal  male placenta


title: Ecoli_Stationary phase in LB T2

description:
Stationary phase in LB, OD 2.8

Ecoli MG1655, stationary phase in LB vs genomic DNA

source_name: Escherichia coli MG1655, Stationary phase in LB OD 2.8


title: Control IgG ChIP_array 31046 in HeLa

description: Control Experiment

source_name: IgG Control ChIP

tag: IgG ChIP


title: Ecoli_Stationary phase in LB T3

description:
Stationary phase in LB, OD 3.1

Ecoli MG1655, stationary phase in LB vs genomic DNA

source_name: Escherichia coli MG1655,  Stationary phase in LB OD 3.1


title: Ecoli_pUC expression OD 0.2

description:
Ecoli DH5alpha, pUC 19 + Amp in LB, OD 0.2 vs no pUC

pUC overexpression

source_name: Escherichia coli DH5alpha (NEB), OD 0.2 in LB, no pUC

source_name: Escherichia coli DH5alpha (NEB), OD 0.2 in LB + Amp,  pUC expression


title: Ecoli_Stationary phase in LB T1

description:
Stationary phase in LB, OD 2.4

Ecoli MG1655, stationary phase in LB vs genomic DNA

source_name: Escherichia coli MG1655 genomic DNA

source_name: Escherichia coli MG1655, Stationary phase in LB OD 2.4


title: P30 Fetal Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23105.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P30 Fetal Normal male placenta

tag: P30 Fetal Normal male placenta


title: Ecoli_pUC expression OD 0.5

description:
Ecoli DH5alpha, pUC 19 + Amp in LB, OD 0.5 vs no pUC

pUC overexpression

source_name: Escherichia coli DH5alpha (NEB), OD 0.5 in LB, no pUC

source_name: Escherichia coli DH5alpha (NEB), OD 0.5 in LB + Amp,  pUC expression


title: Ecoli_Novobiocin treatment (20 ug/ml)

description: Novobiocin (20 ug/ml) in LB, 5 min timepoint vs 0 min

source_name: Escherichia coli LE234 acrD-, LB, 0 min before treatment

tag: Escherichia coli LE234 acrD-, 0 min before treatment in LB

source_name: Escherichia coli LE234 acrD-, 5 min after Novobiocin (20 ug/ml) addition in LB


title: Ecoli_Novobiocin treatment (200 ug/ml)

description: Novobiocin (200 ug/ml) in LB, 5 min timepoint vs 0 min

source_name: Escherichia coli LE234 acrD-, 5 min after Novobiocin (200 ug/ml) addition in LB


title: Ecoli_Gamma treatment T5

description: Gamma treatment in Davis, 60 min timepoint vs 0 min untreated

source_name: Escherichia coli MG1655, Davis, 0 min before treatment

tag: Escherichia coli MG1655, 0 min before treatment, Davis

source_name: Escherichia coli MG1655, 60 min after Gamma treatment in Davis


title: Ecoli_Gamma treatment T3

description: Gamma treatment in Davis, 20 min timepoint vs 0 min untreated

source_name: Escherichia coli MG1655, 20 min after Gamma treatment in Davis


title: Ecoli_Gamma treatment T4

description: Gamma treatment in Davis, 40 min timepoint vs 0 min untreated

source_name: Escherichia coli MG1655, 40min after Gamma treatment in Davis


title: Ecoli_Gamma treatment T1

description: Gamma treatment in Davis, 5 min timepoint vs 0 min untreated

source_name: Escherichia coli MG1655, 5 min after Gamma treatment in Davis


title: Ecoli_Gamma treatment T2

description: Gamma treatment in Davis, 10 min timepoint vs 0 min untreated

source_name: Escherichia coli MG1655, 10 min after Gamma treatment in Davis


title: P27 Amnion Normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35665.gif; format: GIF

source_name: P27 Amnion Normal male placenta

tag: P27 Amnion Normal male placenta


title: Ecoli_Novobiocin treatment (50 ug/ml)

description: Novobiocin (50 ug/ml) in LB, 5 min timepoint vs 0 min

source_name: Escherichia coli LE234 acrD-, 5 min after Novobiocin (50 ug/ml) addition in LB


title: Ecoli_Temperature upshift in gyrBT mutant T4

description: Temperature upshift to 42 C in gyrBT mutant, 20 min vs before upshift

source_name: Escherichia coli W3110gyrb234, LB

tag: Escherichia coli W3110gyrb234, LB

source_name: Escherichia coli W3110gyrb234, LB, 20 min after upshift to 42 C

tag: Escherichia coli W3110gyrb234, LB, 2 min after upshift to 42 C


title: HeLa POLII ChIP_array 30633

description: Localizes POLII in ENCODE region in HeLa cells

source_name: POLII ChIP

tag: N20 Ab

source_name: Matched Total DNA


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T6

description: Anaerobic growth in M9 + glucose + fumarate OD 1.29 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655

tag: Escherichia coli MG1655 Aerobic growth on M9 + glucose + fumarate,OD 0.4

source_name: Escherichia coli MG1655,  OD 1.29 anaerobic growth in M9 + glucose + fumarate ,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T5

description: Anaerobic growth in M9 + glucose + fumarate OD 1.07 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655,  OD 1.07, anaerobic growth in M9 + glucose + fumarate ,


title: P31 Maternal normal male placenta

description:
Simple annotation: Primary human tissue, Placenta
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23102.gif; format: GIF

source_name: PR (Placenta + CRG)

source_name: P31 Maternal normal male placenta

tag: P31 Maternal normal male placenta


title: HeLa POLII ChIP_array 31014

tag: N20 antibody was used;

source_name: matched Total DNA

tag: Cy3 label


title: Control IgG ChIP_array 33552 in HeLa

description:
Control Experiment
IgG ChIP in ENCODE

source_name: IgG ChIP


title: Hela POLII ChIP_array 30516


title: Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T6

description: Anaerobic growth in M9 + glucose OD 1.27 vs Aerobic OD 0.4

tag: Escherichia coli MG1655 Aerobic growth OD 0.4

source_name: Escherichia coli MG1655,  OD 1.27 anaerobic growth in M9 + glucose ,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T4

description: Anaerobic growth in M9 + glucose + fumarate OD 0.85 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655, OD 0.85, anaerobic growth in M9 + glucose + fumarate ,


title: Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T4

description: Anaerobic growth in M9 + glucose OD 0.73 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655, OD 0.73, anaerobic growth in M9 + glucose ,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T1

description: Anaerobic growth in M9 + glucose + fumarate OD 0.15 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655, OD 0.15, anaerobic growth in M9 + glucose + fumarate ,


title: Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T5

description: Anaerobic growth in M9 + glucose OD 1.02 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655,  OD 1.02, anaerobic growth in M9 + glucose ,


title: Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T3

description: Anaerobic growth in M9 + glucose OD 0.34  vs Aerobic OD 0.4

source_name: Escherichia coli MG1655,  OD 0.34, anaerobic growth in M9 + glucose ,


title: Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T2

description: Anaerobic growth in M9 + glucose OD 0.15 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655, OD 0.15, anaerobic growth in M9 + glucose ,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T2

description: Anaerobic growth in M9 + glucose + fumarate OD 0.30 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655, OD 0.30, anaerobic growth in M9 + glucose + fumarate ,


title: MCF7 E2F1 ENCODE_array 31300

description: ChIP-chip experiment

data_processing: minimal; by NimbleGen only

source_name: MCF7 ChIP

tag: Cy5 labeled


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T3

description: Anaerobic growth in M9 + glucose + fumarate OD 0.63  vs Aerobic OD 0.4

source_name: Escherichia coli MG1655,  OD 0.63, anaerobic growth in M9 + glucose + fumarate ,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T4

description: Anaerobic growth in glucose + fumarate,OD 0.70 vs genomic DNA

source_name: Escherichia coli MG1655 genomic DNA

tag: Escherichia coli MG1655 genomic DNA

source_name: Escherichia coli MG1655, OD 0.7, anaerobic growth in M9 + glucose + fumarate,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T5

description: Anaerobic growth in glucose + fumarate,OD 1.2 vs genomic DNA

source_name: Escherichia coli MG1655,  OD 1.2, anaerobic growth in M9 + glucose + fumarate,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T3

description: Anaerobic growth in glucose + fumarate,OD 0.43 vs genomic DNA

source_name: Escherichia coli MG1655,  OD 0.43, anaerobic growth in M9 + glucose + fumarate,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T1

description: Anaerobic growth in glucose + fumarate,OD 0.05 vs genomic DNA

source_name: Escherichia coli MG1655, OD 0.05, anaerobic growth in M9 + glucose + fumarate,


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T6

description: Anaerobic growth in glucose + fumarate,stationary vs genomic DNA

source_name: Escherichia coli MG1655,  stationary phase anaerobic growth in M9 + glucose + fumarate,


title: Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T1

description: Anaerobic growth in M9 + glucose OD 0.08 vs Aerobic OD 0.4

source_name: Escherichia coli MG1655

tag: Escherichia coli MG1655 Aerobic growth on M9 +glucose, OD 0.4

source_name: Escherichia coli MG1655, OD 0.08, anaerobic growth in M9 + glucose ,


title: Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T6

description: Anaerobic growth in glucose, stationary vs genomic DNA

source_name: Escherichia coli MG1655,  stationary phase anaerobic growth in M9 + glucose


title: Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T2

description: Anaerobic growth in glucose + fumarate,OD 0.21 vs genomic DNA

source_name: Escherichia coli MG1655, OD 0.21, anaerobic growth in M9 + glucose + fumarate,


title: Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T5

description: Anaerobic growth in glucose, OD 0.9 vs genomic DNA

source_name: Escherichia coli MG1655,  OD 0.9, anaerobic growth in M9 + glucose


title: Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T4

description: Anaerobic growth in glucose, OD 0.6 vs genomic DNA

source_name: Escherichia coli MG1655, OD 0.6, anaerobic growth in M9 + glucose


title: Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T2

description: Anaerobic growth in glucose, OD 0.2 vs genomic DNA

source_name: Escherichia coli MG1655, OD 0.2, anaerobic growth in M9 + glucose


title: MCF7 E2F1 ChIP_array 31311

description: ChIP-chip experiment

source_name: E2F1 ChIP

tag: Cy5; ChIP-chip

source_name: matched Total DNA


title: Ecoli_pUC expression OD 0.9

description:
Ecoli DH5alpha, pUC 19 + Amp in LB, OD 0.9 vs no pUC

pUC overexpression

source_name: Escherichia coli DH5alpha (NEB), OD 0.9 in LB, no pUC

source_name: Escherichia coli DH5alpha (NEB), OD 0.9 in LB + Amp,  pUC expression


title: Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T3

description: Anaerobic growth in glucose, OD 0.35 vs genomic DNA

source_name: Escherichia coli MG1655 genomic DNA

source_name: Escherichia coli MG1655,  OD 0.35, anaerobic growth in M9 + glucose