title: Expression data of  Colorectal Cancer 13

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 17

status: Public on Feb 28 2007

type: RNA

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

description: Sporadic Ca

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

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

extract_protocol: Surgically isolated nonneoplastic rectal mucosa were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: Tissue

value: Colorecal Cancer


city: Rehovot

first: sagi

last: levy

address: Hertzel

department: Molecular Genetics and Physics of Complex Systems

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: cDNA samples were labeled with Cy3 and Cy5 and combined with blockers: 5?g Herring sperm (Promega), 5?g tRNA (Gibco) and 17.5?g Poly A (Poly A oligos were synthesized with mixed length of 40, 50 and 60 Adenine residues). The labeled cDNAs were concentrated to 40?l using Microcon (Millipore) and 40?l of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs were pre-hybridized by incubating at 42C for 45 minutes in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS. The slides were washed in sterile water and dried by centrifugation (3 minutes, 2000 rpm). The labeled samples were boiled for 5 minutes, centrifuged for 1 minute, hybridized on the slide and placed in a hybridization chamber (Corning) for overnight incubation at 42C. The slides were then washed for 5 minutes at 42C with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by three additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience)and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: Background intensity was subtracted using a Bayesian correction, and the ratios of the two dyes were log2-transformed.Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. The two spots corresponding to each gene were then averaged, and genes for which the two spots were significantly different were declared as missing values (along with other genes which were flagged by the image analysis software or removed by manual inspection).

organism: Saccharomyces cerevisiae

source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (3.08 hours)

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse TranscriptaseRNase H Minus (Promega) and labeled by the indirect amino-allyl method.

growth_protocol: Cells were grown in a glucose-limited chemostat (0.02%) and reached steady state. Glucose was then inoculated into the chemostat to reach a final concentration of 0.04%.

extract_protocol: Cells were collected, pelleted and immediately frozen.Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

tag: Strain

value: WT BY4741, haploid

source_name: Batch culture cells grown in a glucose-limited medium to late log phase

growth_protocol: Overnight cells (SD) were washed, transferred to Glucose-limited medium (0.02%) and grown to late log phase


source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (5.08 hours)


title: Expression data of  Colorectal Cancer 10

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 12

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 9

description: Sporadic Ca


source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (1.08 hours)


title: Expression data of  Colorectal Cancer 14

description: Sporadic Ca


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (19.67 hours)

growth_protocol: Cells were grown in a glucose-limited chemostat (0.02%) and reached steady state. H2O2 (0.6mM) was then inoculated into the chemostat


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (7.73 hours)


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (28.32 hours)


source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (0.25 hours)


title: Expression data of  Colorectal Cancer 8

description: Sporadic Ca


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (13.5 hours)


title: Glucose perturbation in a glucose-limited chemostat ( -1.18 hours)

source_name: Cells grown in a glucose-limited chemostat 1.18 hours before the Glucose perturbation


title: Expression data of  Colorectal Cancer 6

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 11

description: Sporadic Ca


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (1.2 hours)


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (2.83 hours)


title: Expression data of  Colorectal Cancer 7

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 2

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 5

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 4

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 1

description: Sporadic Ca


title: Expression data of  UC 50

description: UC-NonCa

source_name: UC 50

value: Nonneoplastic rectal mucosa


title: Expression data of  Colorectal Cancer 3

description: Sporadic Ca


title: Expression data of  UC 52

description: UC-NonCa

source_name: UC 52


title: Expression data of  UC 53

description: UC-Ca

source_name: UC 53


title: H2O2 perturbation in a glucose-limited chemostat (-0.73 hours)

source_name: Cells grown in a glucose-limited chemostat 0.73 hours before the H2O2 perturbation


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (8.93 hours)

growth_protocol: Cells were grown in a glucose-limited chemostat (0.02%) and reached steady state. NaCl (0.4M) was then inoculated into the chemostat


source_name: Cells upon H2O2 perturbation in a glucose-limited chemostat (0.25 hours)


title: Expression data of  UC 51

description: UC-NonCa

source_name: UC 51


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (6.58 hours)

source_name: Batch culture cells grown in a glucose-limited medium to late log phase


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (5.08 hours)


title: Expression data of  UC 48

description: UC-NonCa

source_name: UC 48


title: Expression data of  UC 49

description: UC-NonCa

source_name: UC 49


title: Expression data of  UC 44

description: UC-NonCa

source_name: UC 44


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (1.75 hours)


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (0.75 hours)


title: Expression data of  UC 42

description: UC-NonCa

source_name: UC 42


title: Expression data of  UC 46

description: UC-NonCa

source_name: UC 46


title: Heat shock perturbation in a glucose-limited chemostat (16.05 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (26.7 hours)

growth_protocol: Cells were grown in a glucose-limited chemostat (0.02%) and reached steady state at 30 degrees (C). The cells were then subjected to heat shock of 39 degrees for 5 hours

growth_protocol: Overnight cells (SD) were washed, transferred to Glucose-limited medium (0.02%) and grown to late log phase at 30 degrees (C)


title: Heat shock perturbation in a glucose-limited chemostat (6.33 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (14.25 hours)


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (3 hours)


title: Expression data of  UC 45

description: UC-NonCa

source_name: UC 45


source_name: Cells upon NaCl perturbation in a glucose-limited chemostat (0.25 hours)


title: NaCl perturbation in a glucose-limited chemostat (-0.73 hours)

source_name: Cells grown in a glucose-limited chemostat 0.73 hours before the NaCl perturbation


title: Heat shock perturbation in a glucose-limited chemostat (3.62 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (4.95 hours)


title: Expression data of  UC 41

description: UC-Ca

source_name: UC 41


title: Heat shock perturbation in a glucose-limited chemostat (5.25 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (8.63 hours)

source_name: Batch culture cells grown in a glucose-limited medium to late log phase


title: Expression data of  UC 47

description: UC-NonCa

source_name: UC 47


title: Expression data of  UC 40

description: UC-Ca

source_name: UC 40


title: Heat shock perturbation in a glucose-limited chemostat (9.63 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (21.48 hours)


title: Heat shock perturbation in a glucose-limited chemostat (1.58 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (2.22 hours)


title: Expression data of  UC 43

description: UC-NonCa

source_name: UC 43


title: Expression data of  UC 37

description: UC-NonCa

source_name: UC 37


title: Expression data of  UC 38

description: UC-NonCa

source_name: UC 38


title: Expression data of  UC 36

description: UC-NonCa

source_name: UC 36


title: Expression data of  UC 39

description: UC-Ca

source_name: UC 39


title: Expression data of  UC 34

description: UC-Ca

source_name: UC 34


title: Heat shock perturbation in a glucose-limited chemostat (0.25 hours)

source_name: Cells upon heat shock perturbation in a glucose-limited chemostat (0.33 hours)


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (21.48 hours)

growth_protocol: Cells were grown in a glucose-limited chemostat (0.02%) and reached steady state. DTT (6mM) was then inoculated into the chemostat


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (26.7 hours)


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (8.63 hours)


title: Heat shock perturbation in a glucose-limited chemostat (-0.27 hours)

source_name: Cells grown in a glucose-limited chemostat 0.78 hours before the heat shock perturbation


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (14.25 hours)


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (2.22 hours)

source_name: Batch culture cells grown in a glucose-limited medium to late log phase


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (4.95 hours)


title: Expression data of  UC 33

description: UC-NonCa

source_name: UC 33


title: Expression data of  UC 32

description: UC-NonCa

source_name: UC 32


title: Expression data of  UC 30

description: UC-NonCa

source_name: UC 30


title: Expression data of  UC 31

description: UC-Ca

source_name: UC 31


title: Expression data of  UC 28

description: UC-Ca

source_name: UC 28


title: Expression data of  UC 27

description: UC-NonCa

source_name: UC 27


title: Expression data of  UC 29

description: UC-NonCa

source_name: UC 29


title: ADH1 deletion mutant grown in glucose (2 hour)

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet DNA microarray scannerand image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was removed by subtracting the mean array intensity and the ratios of the two dyes were log2-transformed. The two spots corresponding to each gene were then averaged, and genes with low intesity were excluded by manual inspection).

growth_protocol: adh1 cells were grown overnight on YPD (2% glucose) to O.D. 0.4, washed and then diluted into either YP-glycerol (2%) or fresh YPD

value: BY4741 ADH1::KANMX, haploid

source_name: ADH1 deletion mutant grown overnight on YPD (glucose)

growth_protocol: adh1 cells were grown overnight on YPD to O.D. 0.4


title: ADH1 deletion mutant grown in glucose (4 hour)


title: ADH1 deletion mutant grown in glucose (30 minutes)


title: ADH1 deletion mutant grown in glycerol (4 hour)


title: DTT perturbation in a glucose-limited chemostat (-0.78 hours)

source_name: Cells grown in a glucose-limited chemostat 0.78 hours before the DTT perturbation


source_name: Cells upon DTT perturbation in a glucose-limited chemostat (0.33 hours)


title: Expression data of  UC 23

description: UC-NonCa

source_name: UC 23


title: Expression data of  UC 25

description: UC-NonCa

source_name: UC 25


title: Expression data of  UC 26

description: UC-NonCa

source_name: UC 26


title: Expression data of  UC 24

description: UC-NonCa

source_name: UC 24


title: Expression data of  UC 22

description: UC-NonCa

source_name: UC 22


title: ADH1 deletion mutant grown in glycerol (1 hour)


title: ADH1 deletion mutant grown in glycerol (30 minutes)


title: ADH1 deletion mutant grown in glycerol (2 hour)


title: Expression data of  UC 19

description: UC-NonCa

source_name: UC 19


title: ADH1 deletion mutant- glycerol vs. glucose at log phase- #2

source_name: ADH1 deletion mutant- grown in glycerol to log phase- #2

growth_protocol: Overnight cells (YPD) were transferred to YP-glycerol and grown to log phase

source_name: ADH1 deletion mutant- grown in glucose to log phase- #2

growth_protocol: Overnight cells (YPD) were transferred to fresh YPD and grown to log phase


title: Expression data of  UC 21

description: UC-NonCa

source_name: UC 21


title: ADH1 deletion mutant- glycerol vs. glucose at log phase- #3

source_name: ADH1 deletion mutant- grown in glycerol to log phase- #3

source_name: ADH1 deletion mutant- grown in glucose to log phase- #3


title: WT BY4741- glycerol vs. glucose at log phase- #1

source_name: WT BY4741- grown in glycerol to log phase- #1

source_name: WT BY4741- grown in glucose to log phase- #1


title: WT BY4741- glycerol vs. glucose at log phase- #2

source_name: WT BY4741- grown in glycerol to log phase- #2

source_name: WT BY4741- grown in glucose to log phase- #2


title: ADH1 deletion mutant- glycerol vs. glucose at log phase- #1

source_name: ADH1 deletion mutant- grown in glycerol to log phase- #1

source_name: ADH1 deletion mutant- grown in glucose to log phase- #1


title: Expression data of  UC 16

description: UC-Ca

source_name: UC 16


title: Expression data of  UC 18

description: UC-NonCa

source_name: UC 18


title: Expression data of  UC 13

description: UC-NonCa

source_name: UC 13


title: Expression data of  UC 17

description: UC-NonCa

source_name: UC 17


title: Expression data of  UC 35

description: UC-NonCa

source_name: UC 35


title: Expression data of  UC 20

description: UC-NonCa

source_name: UC 20


title: Expression data of  UC 14

description: UC-NonCa

source_name: UC 14


title: Expression data of  UC 6

description: UC-NonCa

source_name: UC 6


title: Expression data of  UC 11

description: UC-Ca

source_name: UC 11


title: Expression data of  UC 10

description: UC-NonCa

source_name: UC 10


title: Expression data of  UC 15

description: UC-Ca

source_name: UC 15


title: Expression data of  UC 5

description: UC-NonCa

source_name: UC 5


title: Expression data of  UC 12

description: UC-NonCa

source_name: UC 12


title: Expression data of  UC 7

description: UC-NonCa

source_name: UC 7


title: Expression data of  UC 4

description: UC-NonCa

source_name: UC 4


title: Expression data of  UC 8

description: UC-NonCa

source_name: UC 8


title: HUVEC+ vs. HUVEC+ DAC_TSA

city: Maastricht

first: Debby

last: Hellebrekers

address: P Debyelaan 25

department: Pathology

country: Netherlands

institute: Maastricht University

description: the basic measure of RNA abundance was taken to be the mean intensity over pixels in the identified signal area

hyb_protocol: Hybridizations according to Agilent standard protocol

scan_protocol: standard Agilent scanning protocol (Agilent's feature extraction software A 6.1.1.)

data_processing: Local background, Minimal signal (feature or background), and average of all background areas.

source_name: HUVEC+

label_protocol: Agilent Fluorescent Direct Label kit

extract_protocol: RNeasy protocol for RNA isolation

tag: tumor-conditioned HUVEC

source_name: HUVEC+ DAC_TSA

treatment_protocol: HUVEC cultured in RPMI1640, supplemented with 20% human serum. These cells were tumor-conditioned with 10 ng/ml bFGF and 10 ng/ml VEGF for 6 days. These cells were treated with 200 nM 5-aza-2'deoxycytidine for 48 hrs, followed by treatment with 300 nM trichostatin A for 24 hrs

tag: tumor-conditioned HUVEC treated with 200 nM 5-aza-2'deoxycytidine for 48 hrs, followed by treatment with 300 nM trichostatin A for 24 hrs.


title: Expression data of  UC 9

description: UC-NonCa

source_name: UC 9


title: HUVEC+ DAC_TSA vs. HUVEC+

treatment_protocol: HUVEC cultured in RPMI1640, supplemented with 20% human serum. These cells were tumor-conditioned with 10 ng/ml bFGF and 10 ng/ml VEGF for 6 days. These cells were treated with 5-aza-2'deoxycytidine (200 nM) for 48 hrs, followed by treatment with 300 nM trichostatin A for 24 hrs.

tag: tumor-conditioned HUVEC treated with 5-aza-2'deoxycytidine (200 nM) for 48 hrs, followed by treatment with 300 nM trichostatin A for 24 hrs.

extract_protocol: Protocol RNeasy protocol for RNA isolation


title: Expression data of  UC 2

description: UC-NonCa

source_name: UC 2


title: Expression data of  UC 3

description: UC-NonCa

source_name: UC 3


title: HUVEC- vs. HUVEC+

source_name: HUVEC-

growth_protocol: HUVEC cultured in RPMI 1640, supplemented with 2% human serum, to serum starve the cells.

tag: quiescent HUVEC

growth_protocol: HUVEC cultured in RPMI1640, supplemented with 20% human serum. These cells were tumor-conditioned with 10 ng/ml bFGF and 10 ng/ml VEGF for 6 days.


title: RSV_rep3

status: Public on Feb 27 2007

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technical University Munich

description:
Human bronchial epithelial cells BEAS-2B were stimulated in vitro with 10E8/ml
UV-inactivated P. aeruginosa or S. aureus or with RSV (MOI 1) for 4 h.
h.

hyb_protocol: Standard Affymetrix procedures (see GeneChip® Expression Analysis Technical Manual)

data_processing: Expression VALUES were generated using RMA (Robust Multi-Array Average expression measure) using R 2.4.0; Absolute Detection (ABS_CALL) was generated using the function mas5calls of the affy package for R.

label_protocol: Affymetrix one round amplification

extract_protocol: RNA was isolated using HighPureTM RNA kit (Roche) as recommended by the manufacturer.

tag: bronchial epithelial cells BEAS-2B, RSV stimulated, 4h, replicate 3


title: S_aureus_rep1

scan_protocol: Standard Affymetrix procedures (see GeneChip® Expression Analysis Technical Manual)

tag: bronchial epithelial cells BEAS-2B, S_aureus stimulated, 4h, replicate 1


title: control_rep3

tag: bronchial epithelial cells BEAS-2B, not stimulated, 4h, replicate 3


title: P_aeruginosa_rep2

tag: bronchial epithelial cells BEAS-2B, P_aeruginosa stimulated, 4h, replicate 2


title: RSV_rep2

tag: bronchial epithelial cells BEAS-2B, RSV stimulated, 4h, replicate 2


title: control_rep2

description:
Human bronchial epithelial cells BEAS-2B were stimulated in vitro with 10E8/ml
UV-inactivated P. aeruginosa or S. aureus or with RSV (MOI 1) for 4 h.

tag: bronchial epithelial cells BEAS-2B, not stimulated, 4h, replicate 2


title: HUVEC+ vs. HUVEC-

treatment_protocol: HUVEC cultured in RPMI1640, supplemented with 20% human serum. These cells were tumor-conditioned with 10 ng/ml bFGF and 10 ng/ml VEGF for 6 days.

treatment_protocol: HUVEC cultured in RPMI 1640, supplemented with 2% human serum, to serum starve the cells.


title: Expression data of  UC 1

description: UC-NonCa

source_name: UC 1


title: S_aureus_rep2

tag: bronchial epithelial cells BEAS-2B, S_aureus stimulated, 4h, replicate 2


title: P_aeruginosa_rep1

tag: bronchial epithelial cells BEAS-2B, P_aeruginosa stimulated, 4h, replicate 1


title: RSV_rep1

tag: bronchial epithelial cells BEAS-2B, RSV stimulated, 4h replicate 1


title: control_rep1

tag: bronchial epithelial cells BEAS-2B, not stimulated, replicate 1


title: hypothalamic hamartoma with no CPP_HH3

city: Beaverton

first: Valerie

last: Matagne

state: OR

address: 505 nw 185th Ave

department: Neuroscience

country: USA

institute: OHSU

description: gene expression data derived from a hypothalamic hamartoma of a 5 year-old girl with no central precocious puberty and then considered as a control sample

hyb_protocol: Ten ug of labeled cRNA were hybridized with the Human Genome_U133A GeneChip array (Affymetrix, Santa Clara, CA) containing 18,400 transcripts and variants, including 14,500 well-characterized human genes. After overnight hybridization at 45C each array was washed, stained with streptavidin-phycoerythrin (SAPE, Molecular Probes, Eugene, OR), followed by signal amplification with biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and a final SAPE staining step.

scan_protocol: Software – Affymetrix Microarray Suite 5.0

data_processing: Image processing and expression analysis were performed using Affymetrix Microarray Suite (MAS) 5.0 software. An absolute (single assay) expression analysis was performed for each GeneChip genome array hybridization. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS 5.0, six parameters were examined to assess the overall assay performance: background, noise, average signal, % present, ratio of signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total signal for BioC, BioD and CreX probe sets. Prior to further analysis, array data were globally scaled to a uniform, average target intensity for all assays prior to further analysis. Initial filters removed all absent genes and genes with no change across all data sets.

source_name: HH from a 5 year-old girl

label_protocol: One hundred ng of each total RNA sample was amplified and labelled using the GeneChip Eukaryotic Small Sample Target Labelling Assay Version II (Affymetrix, Santa Clara, CA). This protocol uses two rounds of cDNA synthesis and in vitro RNA transcription to produce amplified, biotinylated cRNA targets. In the first round of RNA amplification, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Integrated DNA Technologies, Coralville, IA); cRNA is synthesized using the MEGAscript High Yield Transcription kit (Ambion, Austin, TX). The unlabeled cRNA is then reverse transcribed in the first strand cDNA synthesis step of the second cycle using random primers. A T7-oligo dT primer is used for the second strand cDNA synthesis to generate double-stranded cDNA containing T7 promoter sequences. biotin-labeled cRNA is transcribed from the second round cDNA using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, Farmingdale, NY).

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Columns according to the manufacturer’s specifications.  RNA quality was assessed by OD reading and size fractionation on 1% formaldehyde agarose gels. In addition, the samples were subjected to electrophoretic trace using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Hypothalamic hamartoma (HH) form a 5 year-old girl with no central precocious puberty (CPP)


title: P_aeruginosa_rep3

tag: bronchial epithelial cells BEAS-2B, P_aeruginosa stimulated, 4h, replicate 3


title: hypothalamic hamartoma with no CPP_HH4

description: gene expression data derived from a hypothalamic hamartoma of a 37 year-old man with no central precocious puberty and then considered as a control sample

source_name: HH from a 37 year-old man

tag: Hypothalamic hamartoma (HH) form a 37 year-old man with no central precocious puberty (CPP)


title: hypothalamic hamartoma with no CPP_HH2

description: gene expression data derived from a hypothalamic hamartoma of a 9 year-old boy with no central precocious puberty and then considered as a control sample

source_name: HH from a 9 year-old boy

tag: Hypothalamic hamartoma (HH) form a 9 year-old boy with no central precocious puberty (CPP)


title: ID_69_TimePt_2

city: Bloomington

first: Milton

middle: W

last: Taylor

state: IN

address: 343 Jordan Hall

department: Biology

institute: Indiana University

description: Gene Expression for human subject. Human PBMC collected from whole blood. PBMC were collected in sodium heparin-CPT tubes at day 0 (before treatment) and days 1, 2, 7, 14 and 28 after initiation of treatment. Whole blood was diluted with an equal volume (8 ml) of phosphate buffered saline (PBS), carefully layered over a 10 ml Ficoll-Hypaque gradient (Amersham/Pharmacia, Piscataway, NJ) and centrifuged at 800 rpm for 20 minutes at room temperature. The buffy coat layer was transferred to a 15ml RNAse-free tube, diluted with PBS, and centrifuged at 100 x g for 15 minutes at room temperature. The supernatants were discarded and the PBMC were retained.

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: The microarrays were scanned using a dedicated Model 3000 scanner controlled by GCOS software.

data_processing: GCOS was used for data processing. The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm

source_name: Human PBMC collected from whole blood.

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out according to the protocols recommended by Affymetrix in the GeneChip® Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)

extract_protocol: Samples were shipped overnight by express courier at 4 degrees C to a central repository where RNA was isolated on arrival  The PBMC were lysed in 1 ml of TRI reagent (Molecular Research Center Inc: Cincinnati, OH). The PBMC lysate was mixed with 1-Bromo-3-chloropropane (BCP)-phase separation agent for 1 minute, and incubated at room temperature for 15 minutes. After centrifugation for 15 minutes at 12,000 rpm and 4 degrees C, RNA was precipitated from the supernatant overnight at -20 degrees C with an equal volume of isopropanol and 1/10 volume of 7.5 M-ammonium acetate. The precipitate was washed twice with 75% ethanol, and then with 95% ethanol. RNA was briefly air-dried and then further purified using RNeasy columns (Qiagen: Valencia, CA).

treatment_protocol: The clinical protocol called for participants to be treated for up to 48 weeks with peginterferon alpha-2a (Pegasys™, Roche Pharmaceuticals Nutley, NJ) in a dose of 180 µg weekly by self-administered subcutaneous injection and ribavirin (Copegus™, Roche) orally in a dose of 1000 or 1200 mg daily based on body weight of less than 75 kg or equal to or greater than 75 kg.


title: hypothalamic hamartoma with CPP_HH1

description: gene expression data derived from a hypothalamic hamartoma of an 8 year-old boy suffering from central precocious puberty and being treated with a GnRH agonist at the time of surgery. This sample is considered as an experimental sample.

source_name: HH from an 8 year-old boy

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Columns according to the manufacturer’s specifications. RNA quality was assessed by OD reading and size fractionation on 1% formaldehyde agarose gels. In addition, the samples were subjected to electrophoretic trace using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: GnRH agonist to treat endocrine manifestations of CPP

tag: Hypothalamic hamartoma (HH) form an 8 year-old boy with central precocious puberty (CPP) at the age of 4 years


title: ID_68_TimePt_28


title: ID_69_TimePt_28


title: ID_69_TimePt_14


title: ID_69_TimePt_1


title: ID_69_TimePt_7


title: ID_69_TimePt_0


title: ID_68_TimePt_14


title: ID_68_TimePt_2


title: ID_68_TimePt_7


title: ID_67_TimePt_2


title: ID_68_TimePt_1


title: ID_67_TimePt_28


title: ID_68_TimePt_0


title: ID_67_TimePt_7


title: ID_67_TimePt_0


title: ID_67_TimePt_14


title: ID_67_TimePt_1


title: ID_66_TimePt_2


title: ID_66_TimePt_28


title: ID_66_TimePt_7


title: ID_66_TimePt_14


title: ID_66_TimePt_1


title: ID_65_TimePt_28


title: ID_65_TimePt_0


title: ID_66_TimePt_0


title: ID_65_TimePt_1


title: ID_65_TimePt_2


title: ID_64_TimePt_2


title: ID_64_TimePt_7


title: ID_65_TimePt_7


title: ID_64_TimePt_28


title: ID_64_TimePt_0


title: ID_62_TimePt_28


title: ID_60_TimePt_28


title: ID_62_TimePt_14


title: ID_64_TimePt_1


title: ID_62_TimePt_2


title: ID_65_TimePt_14


title: ID_64_TimePt_14


title: ID_62_TimePt_7


title: ID_62_TimePt_1


title: ID_60_TimePt_14


title: ID_59_TimePt_7


title: ID_59_TimePt_14


title: ID_60_TimePt_7


title: ID_60_TimePt_1


title: ID_59_TimePt_2


title: ID_58_TimePt_28


title: ID_58_TimePt_14


title: ID_60_TimePt_2


title: ID_60_TimePt_0


title: ID_59_TimePt_1


title: ID_58_TimePt_7


title: ID_59_TimePt_28


title: ID_59_TimePt_0


title: ID_58_TimePt_2


title: ID_58_TimePt_1


title: ID_57_TimePt_28


title: ID_58_TimePt_0


title: ID_57_TimePt_1


title: ID_56_TimePt_14


title: ID_57_TimePt_7


title: ID_57_TimePt_0


title: ID_57_TimePt_2


title: ID_62_TimePt_0


title: ID_56_TimePt_28


title: ID_56_TimePt_7


title: ID_57_TimePt_14


title: ID_55_TimePt_14


title: ID_56_TimePt_2


title: ID_55_TimePt_1


title: ID_55_TimePt_28


title: ID_54_TimePt_0


title: ID_54_TimePt_28


title: ID_55_TimePt_7


title: ID_56_TimePt_0


title: ID_56_TimePt_1


title: ID_55_TimePt_2


title: ID_54_TimePt_1


title: ID_54_TimePt_7


title: ID_55_TimePt_0


title: ID_53_TimePt_28


title: ID_53_TimePt_14


title: ID_54_TimePt_14


title: ID_54_TimePt_2


title: ID_53_TimePt_7


title: ID_53_TimePt_1


title: ID_53_TimePt_2


title: ID_52_TimePt_7


title: ID_52_TimePt_14


title: ID_53_TimePt_0


title: ID_52_TimePt_28


title: ID_52_TimePt_2


title: ID_52_TimePt_1


title: ID_49_TimePt_0


title: ID_49_TimePt_28


title: ID_52_TimePt_0


title: ID_48_TimePt_28


title: ID_48_TimePt_7


title: ID_48_TimePt_1


title: ID_47_TimePt_14


title: ID_48_TimePt_2


title: ID_49_TimePt_2


title: ID_48_TimePt_0


title: ID_47_TimePt_7


title: ID_49_TimePt_1


title: ID_49_TimePt_7


title: ID_49_TimePt_14


title: ID_47_TimePt_28


title: ID_47_TimePt_0


title: ID_47_TimePt_1


title: ID_47_TimePt_2


title: ID_46_TimePt_14


title: ID_48_TimePt_14


title: ID_46_TimePt_28


title: ID_46_TimePt_1


title: ID_46_TimePt_0


title: ID_46_TimePt_7


title: ID_46_TimePt_2


title: ID_45_TimePt_14


title: ID_45_TimePt_28


title: ID_45_TimePt_0


title: ID_45_TimePt_1


title: ID_45_TimePt_7


title: ID_44_TimePt_7


title: ID_43_TimePt_7


title: ID_44_TimePt_0


title: ID_44_TimePt_28


title: ID_43_TimePt_14


title: ID_44_TimePt_1


title: ID_44_TimePt_2


title: ID_42_TimePt_28


title: ID_43_TimePt_28


title: ID_44_TimePt_14


title: ID_42_TimePt_7


title: ID_43_TimePt_0


title: ID_43_TimePt_1


title: ID_43_TimePt_2


title: ID_41_TimePt_7


title: ID_41_TimePt_14


title: ID_42_TimePt_2


title: ID_42_TimePt_1


title: ID_40_TimePt_7


title: ID_41_TimePt_0


title: ID_42_TimePt_0


title: ID_41_TimePt_1


title: ID_42_TimePt_14


title: ID_40_TimePt_2


title: ID_41_TimePt_2


title: ID_40_TimePt_0


title: ID_39_TimePt_2


title: ID_40_TimePt_1


title: ID_39_TimePt_28


title: ID_39_TimePt_14


title: ID_39_TimePt_7


title: ID_39_TimePt_0


title: ID_38_TimePt_1


title: ID_37_TimePt_14


title: ID_38_TimePt_7


title: ID_37_TimePt_28


title: ID_38_TimePt_2


title: ID_38_TimePt_14


title: ID_38_TimePt_0


title: ID_37_TimePt_0


title: ID_36_TimePt_14


title: ID_37_TimePt_1


title: ID_36_TimePt_7


title: ID_38_TimePt_28


title: ID_37_TimePt_2


title: ID_36_TimePt_1


title: ID_37_TimePt_7


title: ID_36_TimePt_2


title: ID_36_TimePt_0


title: ID_35_TimePt_7


title: ID_35_TimePt_2


title: ID_35_TimePt_14


title: ID_35_TimePt_1


title: ID_35_TimePt_28


title: ID_34_TimePt_28


title: ID_36_TimePt_28


title: ID_35_TimePt_0


title: ID_34_TimePt_14


title: ID_34_TimePt_7


title: ID_34_TimePt_0


title: ID_34_TimePt_1


title: ID_32_TimePt_28


title: ID_34_TimePt_2


title: ID_32_TimePt_1


title: ID_32_TimePt_0


title: ID_28_TimePt_28


title: ID_28_TimePt_14


title: ID_29_TimePt_14


title: ID_32_TimePt_2


title: ID_27_TimePt_7


title: ID_28_TimePt_7


title: ID_29_TimePt_2


title: ID_29_TimePt_7


title: ID_28_TimePt_2


title: ID_32_TimePt_7


title: ID_29_TimePt_0


title: ID_28_TimePt_1


title: ID_32_TimePt_14


title: ID_27_TimePt_14


title: ID_29_TimePt_1


title: ID_27_TimePt_28


title: ID_28_TimePt_0


title: ID_27_TimePt_2


title: ID_25_TimePt_14


title: ID_25_TimePt_7


title: ID_27_TimePt_0


title: ID_25_TimePt_28


title: ID_27_TimePt_1


title: ID_25_TimePt_0


title: ID_24_TimePt_28


title: ID_24_TimePt_14


title: ID_23_TimePt_28


title: ID_23_TimePt_2


title: ID_23_TimePt_14


title: ID_24_TimePt_1


title: ID_24_TimePt_2


title: ID_23_TimePt_0


title: ID_21_TimePt_28


title: ID_25_TimePt_1


title: ID_25_TimePt_2


title: ID_24_TimePt_7


title: ID_23_TimePt_1


title: ID_21_TimePt_2


title: ID_23_TimePt_7


title: ID_21_TimePt_7


title: ID_21_TimePt_1


title: ID_21_TimePt_14


title: ID_20_TimePt_28


title: ID_21_TimePt_0


title: ID_20_TimePt_2


title: ID_20_TimePt_1


title: ID_20_TimePt_14


title: ID_20_TimePt_0


title: ID_20_TimePt_7


title: ID_19_TimePt_28


title: ID_18_TimePt_14


title: ID_39_TimePt_1


title: ID_19_TimePt_7


title: ID_18_TimePt_1


title: ID_19_TimePt_0


title: ID_19_TimePt_1


title: ID_17_TimePt_7


title: ID_19_TimePt_2


title: ID_17_TimePt_28


title: ID_18_TimePt_28


title: ID_17_TimePt_1


title: ID_18_TimePt_7


title: ID_17_TimePt_0


title: ID_16_TimePt_2


title: ID_17_TimePt_2


title: ID_18_TimePt_0


title: ID_16_TimePt_1


title: ID_16_TimePt_14


title: ID_19_TimePt_14


title: ID_18_TimePt_2


title: ID_16_TimePt_28


title: ID_17_TimePt_14


title: ID_16_TimePt_7


title: ID_16_TimePt_0


title: ID_15_TimePt_7


title: ID_15_TimePt_14


title: ID_15_TimePt_0


title: ID_14_TimePt_1


title: ID_13_TimePt_2


title: ID_13_TimePt_0


title: ID_14_TimePt_0


title: ID_13_TimePt_28


title: ID_13_TimePt_1


title: ID_15_TimePt_1


title: ID_14_TimePt_28


title: ID_14_TimePt_2


title: ID_15_TimePt_28


title: ID_13_TimePt_7


title: ID_11_TimePt_2


title: ID_12_TimePt_2


title: ID_11_TimePt_1


title: ID_15_TimePt_2


title: ID_14_TimePt_7


title: ID_13_TimePt_14


title: ID_14_TimePt_14


title: ID_12_TimePt_7


title: ID_11_TimePt_7


title: ID_12_TimePt_1


title: ID_12_TimePt_0


title: ID_11_TimePt_0


title: ID_10_TimePt_28


title: ID_10_TimePt_2


title: ID_10_TimePt_7


title: ID_9_TimePt_28


title: ID_10_TimePt_0


title: ID_10_TimePt_14


title: ID_9_TimePt_14


title: ID_9_TimePt_1


title: ID_8_TimePt_2


title: ID_10_TimePt_1


title: ID_8_TimePt_1


title: ID_9_TimePt_2


title: ID_9_TimePt_0


title: ID_7_TimePt_7


title: ID_8_TimePt_7


title: ID_8_TimePt_0


title: ID_6_TimePt_14


title: ID_6_TimePt_2


title: ID_6_TimePt_1


title: ID_7_TimePt_0


title: ID_6_TimePt_28


title: ID_7_TimePt_1


title: ID_5_TimePt_28


title: ID_6_TimePt_0


title: ID_6_TimePt_7


title: ID_4_TimePt_2


title: ID_4_TimePt_7


title: ID_5_TimePt_2


title: ID_3_TimePt_14


title: ID_7_TimePt_2


title: ID_5_TimePt_1


title: ID_3_TimePt_7


title: ID_3_TimePt_2


title: ID_5_TimePt_7


title: ID_5_TimePt_14


title: ID_4_TimePt_14


title: ID_3_TimePt_28


title: ID_5_TimePt_0


title: ID_4_TimePt_1


title: ID_4_TimePt_0


title: ID_2_TimePt_2


title: ID_3_TimePt_1


title: ID_4_TimePt_28


title: ID_3_TimePt_0


title: ID_2_TimePt_1


title: ID_2_TimePt_28


title: ID_2_TimePt_14


title: ID_2_TimePt_7


title: ID_2_TimePt_0


title: universal_reference_vs_6_cell_lines_Namalwa

city: Kyoto

first: Hiromu

last: Takematsu

state: Kyoto

address: Shogoin-Kawahara 53

department: Human Health Science

institute: Kyoto Univ. Sch. of Medicine

description: Gene expression profile of glycan-related genes

hyb_protocol: Labeled probes were mixed together and  loaded onto the microarray and subjected to 65℃ incubation for  16-20hours. The microarray was subsequently washed in 2xSSC, 2xSSC/ 0.2%SDS at55℃ for 5min twice, 2xSSC/0.2%SDS at 65℃  for  5min, 0.05xSSC at room temperature ,and spun for 3min at 600rpm to dry.

scan_protocol: Fluorescence image of the microarray was obtained  using Affymetrix 428 Array Scanner. Image intensity data were  extracted with ImaGene software(BioDiscovery).

data_processing: Spot intensities were corrected for local  background and log2 value of  Cy5/Cy3 were calculated. The normalized  ratio was obtained by calculating the sigma of  each channel. To judged spot reliability, signal intensities were corrected for local  background and spot intensity exceeding threshold value {=Average(back)+2*STDEV(back)} was ruled reliable for each channel. Rank 5 stands for being reliable in both channel, rank 4 for single channel, rank 3 for below threshold in both, rank 2 for taken off from further calculation due to negative value of signal, rank 1 taken off from further calculation due to the noise on the scanned array image.

molecule: polyA RNA

source_name: Human universal reference RNA

label_protocol: 1microgram of polyA+universal reference RNA (ribosomal RNA  contamination subtracted) and lamba-A RNA for spiked control were  subjected to fluorescent labeling with Cy3-dUTP using Cyscribe First- Strand cDNA Labeling kit(Amersham).

extract_protocol: Human Universal RNA were amplified with RiboAmp  RNA Amplification kit (ARCTURUS ,USA). Quality of polyA+RNA and  contamination of ribosomal RNA were assessed using Agilent Lab-on-a- Chip 2100 Bioanalyser (Agilent Technologies, USA).

tag: Human Universal RNA (Clontech, USA)  is a mixture  of RNA from several tissues.

source_name: human B cell line, Namalwa

label_protocol: 1microgram of polyA+RNA from cells(ribosomal RNA  contamination subtracted) and lamba-A RNA for spiked control were  subjected to fluorescent labeling with Cy5-dUTP using Cyscribe First- Strand cDNA Labeling kit(Amersham).

growth_protocol: Human cell lines were maintained  in RPMI1640  supplemented with 10% heat-inactivated FCS, sodium pyruvate, non- essential amino acids solution, L-gulutamine, and 2-mercaptoethanol.

extract_protocol: PolyA+RNA were isolated from cells using mTRAP  mRNA isolation Midi kit(Active Motif, USA). Quality of polyA+RNA and  contamination of ribosomal RNA were assessed using Agilent Lab-on-a- Chip 2100 Bioanalyser(Agilent Technologies, USA).

tag: Namalwa :Burkitt's  lymphoma


title: universal_reference_vs_6_cell_lines_KMS-12PE

source_name: human B cell line, KMS-12PE

value: myeloma from pleural effusion


title: universal_reference_vs_6_cell_lines_Ramos

source_name: human B cell line, Ramos

tag: Ramos

value: Burkitt's  lymphoma


title: universal_reference_vs_6_cell_lines_Raji

source_name: human B cell line, Raji

tag: Raji

value: Burkitt's lymphoma


title: universal_reference_vs_6_cell_lines_KMS-12BM

source_name: human B cell line, KMS-12BM

value: myeloma from bone  marrow


title: ID_1_TimePt_1


title: ID_1_TimePt_7


title: universal_reference_vs_6_cell_lines_(Daudi)

source_name: human B cell line Daudi

label_protocol: 1ug of polyA+RNA from cells(ribosomal RNA  contamination subtracted) and lamba-A RNA for spiked control were  subjected to fluorescent labeling with Cy5-dUTP using Cyscribe First- Strand cDNA Labeling kit(Amersham).

tag: Cell line

value: Daudi, Tissue :Burkitt's lymphoma


title: ID_1_TimePt_0


title: ID_1_TimePt_2


title: Tumor biopsy C9765

status: Public on Feb 26 2007

city: New York

first: Sofia

middle: K

last: Gruvberger-Saal

state: NY

address: 1130 St. Nicholas Ave., ICRC 406

department: Institute for Cancer Genetics

institute: Columbia University

description: Human breast tumor sample

hyb_protocol: Labeled targets were pooled and combined with blocking agents (12 ug poly-dA, 6 ug yeast tRNA, 20 ug Cot-1 DNA), and hybridized to microarray using the Pronto Universal Hybridization System (Corning) for 18 hours in a humidified chamber (Corning) submerged in a 42 C water bath. Slide was washing using the Pronto Universal Hybridization System.

scan_protocol: Scanned using the Agilent DNA Microarray Scanner at 10 micron resolution. The TIFF image was split and analyzed with GenePix 4.1.1.4. Result files were loaded into BioArray Software Environment. Cy3=channel 1, Cy5=channel 2.

data_processing: Data was preprocessed in the BioArray Software Environment. For each channel, the Median FG - Median BG intensity value was used. Features flagged bad/missing during image analysis were removed. Data was normalized using pin-based LOWESS (6 groups of 8 pins/group). Filtering on median Signal-to-Noise ratio was applied, keeping only those datapoints with a ch1median or ch2median SNR>=3. Features that were present in at least 80% of the 100 tumors in the series were kept, all other features were removed. Features with a variation <0.45 SD of log2(ratio) were removed. Genes were then median centered.

label_protocol: 25 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).

extract_protocol: Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by 2nd round of purification using RNeasy kit (Qiagen).

tag: ERalpha Negative;HER2 CISH Positive;CK5/14 Negative

source_name: Stratagene Universal Human Reference

label_protocol: 15 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).

growth_protocol: See Stratagene product # 740000.

extract_protocol: See Stratagene product # 740000.

treatment_protocol: See Stratagene product # 740000.

tag: See Stratagene product # 740000.


title: Tumor biopsy C9174

description: Human breast tumor sample

tag: ERalpha Positive;HER2 CISH Negative;CK5/14 Negative


title: Tumor biopsy C9298

description: Human breast tumor sample

tag: ERalpha Negative;HER2 CISH Not Available;CK5/14 Positive


title: Tumor biopsy C8610

description: Human breast tumor sample

tag: ERalpha Negative;HER2 CISH Negative;CK5/14 Negative


title: Tumor biopsy C8800

description: Human breast tumor sample

tag: ERalpha Negative;HER2 CISH Negative;CK5/14 Positive


title: Tumor biopsy C9795

description: Human breast tumor sample


title: Tumor biopsy C8676

description: Human breast tumor sample


title: Tumor biopsy C9732

description: Human breast tumor sample


title: Tumor biopsy C9552

description: Human breast tumor sample


title: Tumor biopsy C9159

description: Human breast tumor sample

tag: ERalpha Positive;HER2 CISH Not Available;CK5/14 Negative


title: Tumor biopsy C9126

description: Human breast tumor sample


title: Tumor biopsy C9029

description: Human breast tumor sample


title: Tumor biopsy C8860

description: Human breast tumor sample


title: Tumor biopsy C9016

description: Human breast tumor sample


title: Tumor biopsy C8582

description: Human breast tumor sample


title: Tumor biopsy C8560

description: Human breast tumor sample


title: Tumor biopsy C8401

description: Human breast tumor sample


title: Tumor biopsy C8477

description: Human breast tumor sample


title: Tumor biopsy C8537

description: Human breast tumor sample

tag: ERalpha Positive;HER2 CISH Positive;CK5/14 Negative


title: Tumor biopsy C8290

description: Human breast tumor sample


title: Tumor biopsy C8333

description: Human breast tumor sample


title: Tumor biopsy C7956

description: Human breast tumor sample


title: Tumor biopsy C8237

description: Human breast tumor sample


title: Tumor biopsy C8196

description: Human breast tumor sample


title: Tumor biopsy C8212

description: Human breast tumor sample


title: Tumor biopsy C8174

description: Human breast tumor sample


title: Tumor biopsy C7493

description: Human breast tumor sample


title: Tumor biopsy C7845

description: Human breast tumor sample


title: Tumor biopsy C7609

description: Human breast tumor sample


title: Tumor biopsy C7921

description: Human breast tumor sample


title: Tumor biopsy C7583

description: Human breast tumor sample


title: Tumor biopsy C7495

description: Human breast tumor sample


title: Tumor biopsy C7722

description: Human breast tumor sample


title: Tumor biopsy C7589

description: Human breast tumor sample


title: Tumor biopsy C7549

description: Human breast tumor sample


title: ID_9_TimePt_7


title: Tumor biopsy C7604

description: Human breast tumor sample


title: Tumor biopsy C7519

description: Human breast tumor sample


title: Tumor biopsy C7811

description: Human breast tumor sample

tag: ERalpha Negative;HER2 CISH Positive;CK5/14 Positive


title: Tumor biopsy C7688

description: Human breast tumor sample


title: Tumor biopsy C7632

description: Human breast tumor sample


title: Tumor biopsy C7461

description: Human breast tumor sample


title: Tumor biopsy C7490

description: Human breast tumor sample


title: Tumor biopsy C7408

description: Human breast tumor sample


title: Tumor biopsy C7422

description: Human breast tumor sample


title: Tumor biopsy C7246

description: Human breast tumor sample


title: Tumor biopsy C7357

description: Human breast tumor sample


title: Tumor biopsy C7244

description: Human breast tumor sample


title: Tumor biopsy C7366

description: Human breast tumor sample


title: Tumor biopsy C7367

description: Human breast tumor sample


title: Tumor biopsy C7168

description: Human breast tumor sample


title: Tumor biopsy C7170

description: Human breast tumor sample


title: Tumor biopsy C6773

description: Human breast tumor sample


title: Tumor biopsy C7151

description: Human breast tumor sample


title: Tumor biopsy C6716

description: Human breast tumor sample


title: Tumor biopsy C7102

description: Human breast tumor sample


title: Tumor biopsy C7035

description: Human breast tumor sample


title: Tumor biopsy C7106

description: Human breast tumor sample


title: Tumor biopsy C6617

description: Human breast tumor sample


title: Tumor biopsy C6366

description: Human breast tumor sample


title: Tumor biopsy C6616

description: Human breast tumor sample


title: Tumor biopsy C6464

description: Human breast tumor sample


title: Tumor biopsy C6474

description: Human breast tumor sample


title: Tumor biopsy C6257

description: Human breast tumor sample


title: Tumor biopsy C6557

description: Human breast tumor sample


title: Tumor biopsy C6206

description: Human breast tumor sample

tag: ERalpha Positive;HER2 CISH Positive;CK5/14 Positive


title: Tumor biopsy C6158

description: Human breast tumor sample


title: Tumor biopsy C6687

description: Human breast tumor sample


title: Tumor biopsy C6516

description: Human breast tumor sample


title: Tumor biopsy C6188

description: Human breast tumor sample


title: Tumor biopsy C6165

description: Human breast tumor sample

tag: ERalpha Negative;HER2 CISH Not Available;CK5/14 Negative


title: Tumor biopsy C6219

description: Human breast tumor sample


title: Tumor biopsy C6125

description: Human breast tumor sample


title: Tumor biopsy C6144

description: Human breast tumor sample


title: Tumor biopsy C6537

description: Human breast tumor sample


title: Tumor biopsy C6110

description: Human breast tumor sample


title: Tumor biopsy C6061

description: Human breast tumor sample


title: Tumor biopsy C6047

description: Human breast tumor sample


title: Tumor biopsy C6042

description: Human breast tumor sample


title: Tumor biopsy C6014

description: Human breast tumor sample


title: Tumor biopsy C11829

description: Human breast tumor sample


title: Tumor biopsy C6146

description: Human breast tumor sample


title: Tumor biopsy C13351

description: Human breast tumor sample


title: Tumor biopsy C6021

description: Human breast tumor sample


title: Tumor biopsy C11591

description: Human breast tumor sample


title: Tumor biopsy C10881

description: Human breast tumor sample


title: Tumor biopsy C11968

description: Human breast tumor sample


title: Tumor biopsy C10419

description: Human breast tumor sample


title: Tumor biopsy C11205

description: Human breast tumor sample


title: Tumor biopsy C10580

description: Human breast tumor sample


title: Tumor biopsy C11570

description: Human breast tumor sample


title: Tumor biopsy C11460

description: Human breast tumor sample


title: Tumor biopsy C11620

description: Human breast tumor sample


title: Tumor biopsy C10289

description: Human breast tumor sample


title: Tumor biopsy C10481

description: Human breast tumor sample


title: Tumor biopsy C10607

description: Human breast tumor sample


title: Tumor biopsy C10879

description: Human breast tumor sample


title: Tumor biopsy C10591

description: Human breast tumor sample


title: Tumor biopsy C10109

description: Human breast tumor sample


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 1.000 with mevinolin, Array 8631

status: Public on Feb 23 2007

city: Seattle

first: Marc

last: Facciotti

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 1.000 in standard growth media with 20microgram/ml mevinolin versus standard reference

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See the ISB Microarray Facility website for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see the ISB Microarray Pipeline webpage for more details

label: Alexa 547

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC1, reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-356

growth_protocol: Mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1 grown in standard growth media

label: Alexa 647

source_name: Halobacterium NRC1, tfbG expression from plasmid pMTFcmyc

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbG grown in standard growth media with mevinolin


title: Tumor biopsy C10426

description: Human breast tumor sample


title: Tumor biopsy C10335

description: Human breast tumor sample


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.180 with mevinolin, Array 8414

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.180 in standard growth media with 20microgram/ml mevinolin versus standard reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-346


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.946 with mevinolin, Array 8852

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.946 in standard growth media with 20microgram/ml mevinolin versus standard reference

source_name: Halobacterium NRC1, tfbF expression from plasmid pMTFcmyc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-341

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbF grown in standard growth media with mevinolin

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.918 with mevinolin, Array 8855

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.918 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-344


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 1.114 with mevinolin, Array 8759

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 1.114 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-340

source_name: Halobacterium NRC1, tfbC expression from plasmid pMTFcmyc

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbC grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing _tfb grown to OD600 _1.08 with mevinolin, Array 8756

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing _tfb grown to OD600 _1.08 in standard growth media with 20microgram/ml mevinolin versus standard reference

source_name: Halobacterium NRC1, _tfb expression from plasmid pMTFcmyc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-337

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor _tfb grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.946 with mevinolin, Array 8853

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-342

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.946 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.408 with mevinolin, Array 8503

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.408 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-350


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.433 with mevinolin, Array 8513

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.433 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-352


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 1.000 with mevinolin, Array 8630

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-355

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 1.000 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.433 with mevinolin, Array 8512

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-351

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.433 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.408 with mevinolin, Array 8502

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-349

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.408 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 1.080 with mevinolin, Array 8615

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 1.080 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-354


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.180 with mevinolin, Array 8413

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-345

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.180 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 1.080 with mevinolin, Array 8614

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-353

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 1.080 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.918 with mevinolin, Array 8854

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-343

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.918 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 1.114 with mevinolin, Array 8758

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-339

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 1.114 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.872 with mevinolin, Array 8753

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.872 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-334

source_name: Halobacterium NRC1, tfbB expression from plasmid pMTFcmyc

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbB grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing _tfb grown to OD600 _1.08 with mevinolin, Array 8757

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-338

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing _tfb grown to OD600 _1.08 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.872 with mevinolin, Array 8752

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-333

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.872 in standard growth media with 20microgram/ml mevinolin

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 1.041 with mevinolin, Array 8755

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 1.041 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-336


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.170 with mevinolin, Array 8493

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.170 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-348


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 1.041 with mevinolin, Array 8754

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-335

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 1.041 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbG grown to OD600 0.170 with mevinolin, Array 8492

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-347

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbG grown to OD600 0.170 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.976 with mevinolin, Array 8751

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.976 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-332

source_name: Halobacterium NRC1, tfbA expression from plasmid pMTFcmyc

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbA grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.983 with mevinolin, Array 8749

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.983 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-330


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.976 with mevinolin, Array 8750

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-331

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.976 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.821 with mevinolin, Array 8747

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.821 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-328


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.888 with mevinolin, Array 8734

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.888 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-315


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.983 with mevinolin, Array 8748

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-329

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.983 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.880 with mevinolin, Array 8743

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.880 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-324


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.814 with mevinolin, Array 8736

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.814 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-317


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.908 with mevinolin, Array 8732

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.908 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-313


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.814 with mevinolin, Array 8737

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-318

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.814 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.820 with mevinolin, Array 8744

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.820 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-325


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.840 with mevinolin, Array 8739

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.840 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-320


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.820 with mevinolin, Array 8745

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-326

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.820 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.470 with mevinolin, Array 8729

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.470 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-312

growth_protocol: Mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.490 with mevinolin, Array 8727

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.490 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-310


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.880 with mevinolin, Array 8742

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-323

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.880 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.470 with mevinolin, Array 8728

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-311

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.470 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.821 with mevinolin, Array 8746

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-327

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.821 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.857 with mevinolin, Array 8740

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.857 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-321


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.840 with mevinolin, Array 8738

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-319

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.840 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.888 with mevinolin, Array 8735

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-316

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.888 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.490 with mevinolin, Array 8726

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-309

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.490 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.908 with mevinolin, Array 8733

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-314

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.908 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.394 with mevinolin, Array 8723

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.394 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-306


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.857 with mevinolin, Array 8741

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-322

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.857 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.430 with mevinolin, Array 8724

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.430 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-307


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.430 with mevinolin, Array 8725

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-308

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.430 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.394 with mevinolin, Array 8722

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-305

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.394 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.496 with mevinolin, Array 8721

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.496 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-304


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.448 with mevinolin, Array 8719

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.448 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-302

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.496 with mevinolin, Array 8720

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-303

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.496 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.412 with mevinolin, Array 8714

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.412 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-297


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.448 with mevinolin, Array 8718

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-301

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.448 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.412 with mevinolin, Array 8715

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-298

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.412 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.198 with mevinolin, Array 8711

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.198 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-294


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.148 with mevinolin, Array 8709

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.148 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-292


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.157 with mevinolin, Array 8703

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.157 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-286


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.198 with mevinolin, Array 8710

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-293

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.198 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.180 with mevinolin, Array 8713

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.180 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-296


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.399 with mevinolin, Array 8717

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.399 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-300


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.141 with mevinolin, Array 8633

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.141 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-282


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.144 with mevinolin, Array 8634

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.144 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-283


title: Knockout of transcription factor ura3grown to OD600 0.853 in standard growth media, Array 9542

description: knockout of transcription factor ura3grown to OD600 0.853 in standard growth media

source_name: Halobacterium NRC1, ura3 knockout strain

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-279

tag: knockout of transcription factor ura3 grown in standard growth media


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.399 with mevinolin, Array 8716

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-299

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.399 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.157 with mevinolin, Array 8702

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-285

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.157 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbF grown to OD600 0.180 with mevinolin, Array 8712

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-295

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbF grown to OD600 0.180 in standard growth media with 20microgram/ml mevinolin

growth_protocol: Mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.132 with mevinolin, Array 8706

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.132 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-289

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.141 with mevinolin, Array 8632

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-281

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.141 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.152 with mevinolin, Array 8704

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.152 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-287


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.148 with mevinolin, Array 8708

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-291

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.148 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbA grown to OD600 0.144 with mevinolin, Array 8636

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-284

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbA grown to OD600 0.144 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbC grown to OD600 0.132 with mevinolin, Array 8707

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-290

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbC grown to OD600 0.132 in standard growth media with 20microgram/ml mevinolin


title: Knockout of transcription factor tfbDgrown to OD600 0.871 in standard growth media, Array 9537

description: knockout of transcription factor tfbDgrown to OD600 0.871 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-278

source_name: Halobacterium NRC1, tfbD knockout

tag: knockout of transcription factor tfbD grown in standard growth media


title: Knockout of transcription factor ura3grown to OD600 0.853 in standard growth media, Array 9543

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-280

growth_protocol: knockout of transcription factor ura3grown to OD600 0.853 in standard growth media


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbB grown to OD600 0.152 with mevinolin, Array 8705

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-288

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbB grown to OD600 0.152 in standard growth media with 20microgram/ml mevinolin


title: Knockout of transcription factor tfbDgrown to OD600 0.871 in standard growth media, Array 9536

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-277

growth_protocol: knockout of transcription factor tfbDgrown to OD600 0.871 in standard growth media


title: Knockout of transcription factor tfbDgrown to OD600 0.876 in standard growth media, Array 9534

description: knockout of transcription factor tfbDgrown to OD600 0.876 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-275


title: Knockout of transcription factor tfbDgrown to OD600 0.876 in standard growth media, Array 9535

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-276

growth_protocol: knockout of transcription factor tfbDgrown to OD600 0.876 in standard growth media


title: Knockout of transcription factor tfbBgrown to OD600 0.934 in standard growth media, Array 9533

description: knockout of transcription factor tfbBgrown to OD600 0.934 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-274

source_name: Halobacterium NRC1, tfbB knockout

tag: knockout of transcription factor tfbB grown in standard growth media


title: Knockout of transcription factor tfbBgrown to OD600 0.792 in standard growth media, Array 9531

description: knockout of transcription factor tfbBgrown to OD600 0.792 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-272