title: RpoS 11hr 4

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62123.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.49; Parameter Scan Time = 12:22:55; Parameter PMT Volts = 490; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.07; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.49; Parameter Scan Time = 12:22:55; Parameter PMT Volts = 690; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200009; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.18; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen


title: RpoS 11hr 1

status: Public on Nov 03 2006

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62120.gif

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.18; Parameter Scan Time = 11:54:20; Parameter PMT Volts = 490; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200419; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.05; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.18; Parameter Scan Time = 11:54:20; Parameter PMT Volts = 720; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 199980; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen

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

molecule: total RNA

organism: Vibrio cholerae

label_protocol: not provided

extract_protocol: not provided

source_name: RpoS 11hr 2

tag: RpoS 11hr 2


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide01 (C-T1)

city: Brookings

first: Xiuqing

last: Wang

state: SD

address: NPB 252, SDSU

department: Department of Biology and Microbiology

institute: South Dakota State University

description: The goal of the study was to uncover the molecular mechanism of mucosal immunity development using avian infectious bronchitis virus (IBV) as a model system. To achieve this goal, we monitored the kinetics of local gene transcription profiles in trachea tissues after administration of animals with an attenuated IBV strain (IBV-Mass) using chicken 13K cDNA Microarray. More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were characterized. There are total 9 groups including 8 time points for vaccinated groups and 1 pooled age-matched control group. RNAs from each group were used to compare with RNAs from other four groups as determined by the loop-design. Four different RNA samples at each time point were used for hybridization with the respective four other groups. The use of the loop-design allows the direct comparisons between the 9 groups, which would enhance the statistical power and lower the variation. This design is preferred over other methods when the goal of the study is to uncover the kinetics of gene transcription profiles.

hyb_protocol: Hybridization was performed based on the protocol provided by FHCRC (http://www.fhcrc.org/science/shared_resources/genomics/dna_array/spotted_arrays/chicken_array/HybridizationWashProtocol.pdf) with slight modifications. Briefly, nonfat milk was used in pre-hybridization to block non-specific binding sites. For hybridization, the mixture of 20X SSC (6.0µl), 2% SDS (2.4µl) and labeled cDNA samples (5µg for each) was applied to 13k array slide. The total volume was 60µl. Slide was incubated at 63°C for 4hrs followed by incubating at 55°C for 11hrs.

scan_protocol: After washing, slides were dried by quick spin and ready for scanning. Arrays were scanned using a GenePix 4000B Microarray Scanner (Molecular Device Corporation, Sunnyvale, CA) and image analysis was performed by using GenePixPro6.0.

data_processing: Data were collected using GenePixPro6.0 with the LOWESS normalization.

organism: Gallus gallus

source_name: C (pooled common conference)

label_protocol: Message RNA amplification was carried out  with MessageAmp aminoallyl Amplification Kit (Ambion, #1752). Then, amplified RNA was used for cDNA synthesis, which was subsequently labeled with Cy3 and Cy5 Monoreactive dye (Amersham, # PA23001 and # PA25001). Purification of the cDNA was performed with QIAquick PCR Purification Kit (QIAGEN, #28104). All procedures were performed by following the manufacturers’ instructions.

extract_protocol: Total RNA was extracted from the pooled samples of age-matched control and vaccinated chickens using RNeasy mini tissue kit from QIAGEN Inc. (Valencia, CA). Residue DNA was removed with RNase-free DNase (QIAGEN). The concentration of total RNA was determined using NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). The quality and quantity of selected RNA samples was examined by gel electrophoresis.

tag: Ti

value: RNA derived from chicken trachea tissues at day i (i=1,3,5,8,12,21,22,24) after the initial IBV-Mass inoculation; Ci:Control RNA derived from chicken trachea tissue at day i after inoculation with sterile distilled water.

tag: Note

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. We used pooled control RNA for hybridization.


title: cfw90_1_kg

city: Toulouse

first: Serguei

last: Sokol

address: 135 av de Rangueil

department: Lab. Biotech. and Bioprocess

country: France

institute: INSA

description: Yeast treated at calcofluor  (0.02mg/ml) vs non treated. 90 min from the start of treatment.

data_processing: VALUE=log(CH1/CH2)-K, where CH1=max(10,CH1_SIG_MEDIAN-CH1_BKD_MEDIAN), same for CH2. K - is a normalization coefficient K=mean_over_all_spots(log(CH1/CH2))

organism: Saccharomyces cerevisiae

tag: 'drug

value: calcofluor white', 'time:90 min', 'concentration:0.02mg/ml'

value: calcofluor white', 'time:90 min', 'concentration:0mg/ml'


title: Gene Transcription Profile of Local Innate and Adaptive Immunity During Early Phase of IBV Infection Slide3 (T3-C3)

description: To understand the mechanistic basis of local innate and adaptive immunity against infectious bronchitis virus (IBV) at the molecular level, we examined the gene transcription profile of tracheal epithelial layers at 3 days after infection of chickens with an attenuated IBV-Massachusetts strain. For the DNA microarray experiment, total RNA was reverse transcribed and labeled with Cy3 and Cy5 fluorescent dyes and hybridized to the chicken 13K cDNA microarray (FHCRC, Seattle, WA) which contains 13,000 genes derived from both embryonic and adult chicken tissues including immune genes. The experiment was repeated four times using swapped Cy3 or Cy5 dye labeling.

value: RNA derived from chicken trachea tissues 3 days after the initial IBV-Mass inoculation.

value: Control RNA derived from chicken trachea tissue 3 days after inoculation with sterile distilled water.


title: 2005-10-20-81CC44-Chung-HumanX3P-Rep1

status: Public on Nov 02 2006

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

description: frozen biopsy from HNSCC

data_processing: quantile normalization of CEL file, GCRMA estimation of probesets, log2 transformation

label: ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA)

organism: Homo sapiens

source_name: frozen biopsy from HNSCC

extract_protocol: Arcturus Paradise kit

tag: frozen biopsy from HNSCC


title: short term cultured GBM_ID GLI56T1_5`aza-dc_96h_rep1

city: Berlin

first: Wolf

middle: C

last: Mueller

address: Amrumer Str. 1

department: Neuropathology

country: Germany

institute: Charité Universitätsmedizin Berlin

description: short term cultured glioblastoma sample_ID GLI56_treated with 5`aza-dC for 96h_replica 1

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: short term cultured GBM_ID GLI56_5`aza-dc_96h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells were cultured in L-Glutamine free DMEM. Supplement with 1% L-Glutamine, heat inactivated 10%FBS, 1% Penicillin/Streptomycin. Grown in a 37° humidified atmosphere of 5% CO2/95%air.

extract_protocol: TRIzol extraction (Invitrogen Life Technologies) followed by clean-up using RNaesy Mini kit (Quiagen) according to manufacturers instructions.

treatment_protocol: 16h after seeding the cells were treated with 5umol 5`aza-dC for 96h.

tag: short term cultured glioblastoma_GLI56_passage 15


title: short term cultured GBM_ID GLI56T2_5`aza-dc_96h_rep2

description: short term cultured glioblastoma in passage 15_IDGLI56T2_treated with 5`aza-dC for 96h_16h after seeding_replica 2

tag: short term cultured glioblastoma_passage 15


title: cfw5_2_kg

description: Yeast treated at calcofluor  (0.1mg/ml) vs non treated. 5 min from the start of treatment.

value: calcofluor white', 'time:5 min', 'concentration:0.1mg/ml'

value: calcofluor white', 'time:5 min', 'concentration:0mg/ml'


title: 2005-07-19-81CC28-Chung-HuX3P-Rep1

description: HNSCC from FFPE block

source_name: HNSCC from FFPE block

tag: HNSCC from FFPE block


title: Gene Transcription Profile of Local Innate and Adaptive Immunity during Early Phase of IBV Infection Slide4 (T3-C3)


title: cfw5_1_kg

value: calcofluor white', 'time:5 min', 'concentration:0.02mg/ml'


title: 2005-10-20-81CC41-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-07-19-81CC30-Chung-HuX3P-Rep1

description: frozen biopsy from HNSCC


title: 2005-10-20-81CC43-Chung-HumanX3P-Rep1

description: frozen biopsy from HNSCC


title: 2005-10-20-81CC42-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-07-19-81CC29-Chung-HuX3P-Rep1

description: HNSCC from FFPE block


title: 2005-06-02-81CC2-Chung-HuX3P-Rep1

description: frozen biopsy from HNSCC


title: 23-24 hour embryo

city: New Haven

first: Christopher

middle: E

last: Mason

state: CT

address: 1 Gilbert Street

department: Genetics

institute: Yale University

description: Time points were collected on apple juice plates

hyb_protocol: hybridized to these arrays at 52oC.

scan_protocol: Axon Instruments, Genepix scanner 4200, normalized distribution of Cy3 and Cy5 intensities, flagged bad spots.

data_processing: ratio normalized within Yale Microarray Database

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: 23-24 hour embryo

label_protocol: After verification of RNA/DNA content by a spectrophotometer, samples for the six major life stages were mixed to incorporate among-culture and stage variation, then aliquoted into 2g solutions for hybridization. Total RNA from flies of both sexes and species was extracted in Trizol Reagent (GibcoBRL). Poly A+ mRNA was purified using the Oligo-dT cellulose column mRNA kit (Ambion, Inc.).  mRNA was reverse-transcribed at 42oC in the presence of oligodeothymidine and random hexamers, and the labeled cDNA was hybridized to these arrays at 52oC.

extract_protocol: Oligo-dT column

source_name: reference set


title: 19-20 hour embryo

source_name: 19-20 hour embryo

label_protocol: After verification of RNA/DNA content by a spectrophotometer, samples for the six major life stages were mixed to incorporate among-culture and stage variation, then aliquoted into 2g solutions for hybridization. Total RNA from flies of both sexes and species was extracted in Trizol Reagent (GibcoBRL). Poly A+ mRNA was purified using the Oligo-dT cellulose column mRNA kit (Ambion, Inc.).  mRNA was reverse-transcribed at 42oC in the presence of oligodeothymidine and random hexamers, and the labeled cDNA was


title: 2005-03-16-CHC150-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-07-19-81CC1-Chung-HuX3P-Rep2

description: HNSCC from FFPE block


title: 2005-07-19-81CC25-Chung-HuX3P-Rep1

description: HNSCC from FFPE block


title: 21-22 hour embryo

source_name: 21-22 hour embryo


title: 2005-10-20-81CC45-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-03-16-CHC149-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-07-19-81CC26-Chung-HuX3P-Rep1

description: HNSCC from FFPE block


title: 22-23 hour embryo

source_name: 22-23 hour embryo


title: 20-21 hour embryo

source_name: 20-21 hour embryo


title: 2005-06-02-81CC3-Chung-HuX3P-Rep1

description: HNSCC from FFPE block


title: 2005-07-19-81CC27-Chung-HuX3P-Rep1

description: frozen biopsy from HNSCC


title: 18-19 hour embryo

source_name: 18-19 hour embryo


title: 2005-03-16-CHC148-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 17-18 hour embryo

source_name: 17-18 hour embryo


title: 2005-01-27-CHC110-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 13-14 hour embryo

source_name: 13-14 hour embryo


title: 15-16 hour embryo

source_name: 15-16 hour embryo


title: 14-15 hour embryo

source_name: 14-15 hour embryo


title: 16-17 hour embryo

source_name: 16-17 hour embryo


title: 2005-01-27-CHC109-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-01-12-CHC94-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-01-12-CHC93-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-01-14-CHC96-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-01-12-CHC95-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 11-12 hour embryo

source_name: 11-12 hour embryo


title: 12-13 hour embryo

source_name: 12-13 hour embryo


title: 2005-01-12-CHC92-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2005-01-12-CHC91-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: Snail 2 - Cy3

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

description: MDCK epithelial cells transfectant hybridized against MDCK-CMV control.

data_processing: GenePix Pro 6.0

organism: Canis lupus familiaris

source_name: MDCK - CMV

source_name: MDCK - Snail 2


title: 7-8 hour embryo

source_name: 7-8 hour embryo


title: Snail 2 - Cy5

source_name: MCDK - Snail 2


title: 8-9 hour embryo

source_name: 8-9 hour embryo

source_name: reference set


title: Snail 1 - Cy5

source_name: MDCK - Snail 1


title: 2005-01-12-CHC90-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block

source_name: HNSCC from FFPE block


title: 9-10 hour embryo

source_name: 9-10 hour embryo


title: 5-6 hour embryo

source_name: 5-6 hour embryo


title: 2005-01-11-CHC89-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2004-12-16-CHC85-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 6-7 hour embryo

source_name: 6-7 hour embryo


title: Snail 1 - Cy3


title: Slug 2 - Cy3

source_name: MDCK - Slug 2


title: 5.5-6.5 hour embryo

source_name: 5.5-6.5 hour embryo


title: 10-11 hour embryo

source_name: 10-11 hour embryo


title: 2-3 hour embryo

source_name: 2-3 hr embryo

extract_protocol: Olig-dT column


title: 2004-12-16-CHC86-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 3-4 hour embryos

source_name: 3-4 hour embryos


title: 1.5-2.5 hour

source_name: 1.5-2.5 hour embryos


title: 3.5-4.5 hour embryos

source_name: 3.5-4.5 hour embryos


title: 4.5-5.5 hour embryos

source_name: 4.5-5.5 hour embryos


title: E47 1 - Cy5

source_name: MDCK - E47 1

source_name: MDCK - CMV


title: E47 1 - Cy3


title: 4-5 hour embryo

source_name: 4-5 hour embryo


title: Slug 1 - Cy5

source_name: MDCK - Slug 1


title: Slug 2 - Cy5


title: 2004-11-24-CHC81-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2004-12-16-CHC83-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2004-12-16-CHC84-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: E47 2 - Cy5

source_name: MDCK - E47 2


title: 2.5-3.5 hour embryos

source_name: 2.5-3.5 hour embryos

source_name: reference set


title: Slug 1 - Cy3


title: 2004-11-24-CHC80-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block

source_name: HNSCC from FFPE block


title: 2004-11-24-CHC78-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2004-11-24-CHC74-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2004-06-08-300148-Chung-HumanX3P-Rep1

description: frozen biopsy from HNSCC

source_name: frozen biopsy from HNSCC


title: 2004-06-08-S0324497-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: E47 2 - Cy3


title: 2004-11-24-CHC77-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: 2004-11-24-CHC82-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: Anti EGFR Ab and IL-13 vs. Control 2

status: Public on Nov 01 2006

city: San Francisco

first: Agnes

last: Paquet

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description: Normal human bronchial epithelial (NHBE) cells were cultured on air-liquid interface for 14 days and were treated with IL-13, anti-EGFR antibody or both during the final 48 h of culture.

hyb_protocol: http://www.arrays.ucsf.edu/protocols/cDNA Transcription, Labeling and Hybridization.pdf http://www.arrays.ucsf.edu/protocols/cDNA Transcription, Labeling and Hybridization.pdf

scan_protocol: http://www.arrays.ucsf.edu/protocols/genepix_protocol.pdfFluorescence in the Cy3 and Cy5 channels was acquired using an Axon 4000B microarray scanner and GenePix software (Axon Instruments).

data_processing: Data were normalized using print-tip loess normalization, caried out using the Bioconductor package marray. Values indicate the difference in gene expression on a log2 scale. This value is calculated as M = log2(R/G), where R and G are the intensity for the Cy5 and Cy3 channels, erspectively (e.g.: M = 1 indicates 2-fold higher expression in the sample that was labeled with the Cy3 dye, and M = 0 indicates equal expression in both samples). No background subtraction was performed. “A” indicates the total signal intensity of a given spot on the microarray. This value is calculated as A = ½*log2(R*G).

source_name: Anti EGFR Ab and IL-13

label_protocol: http://www.arrays.ucsf.edu/protocols/cDNA Transcription, Labeling and Hybridization.pdf. Preparation of aminoallyl-UTP labeled whole lung aRNA was performed as previously described. Total RNA from tracheal perfusate (1.0 - 1.5 g per sample) was amplified and labeled with aminoallyl-dUTP using the MessageAmp aRNA kit (Ambion). Labeled aRNAs were coupled to Cy3 or Cy5 dyes (CyScribe, Amersham Biosciences) and purified as described.

tag: NHBE cells treated with Anti EGFR Ab and IL-13

source_name: Control

tag: NHBE cells control conditions


title: 2004-11-24-CHC76-Chung-HumanX3P-Rep1

description: HNSCC from FFPE block


title: Anti EGFR Ab and IL-13 vs. Control 1

source_name: Anti EGFR Ab with IL-13

tag: NHBE cells treated with Anti EGFR Ab with IL-13


title: Anti EGFR Ab No IL-13 vs. Control 3

source_name: Anti EGFR Ab No IL-13

tag: NHBE cells treated with Anti EGFR Ab No IL-13


title: IL-13 vs. Control 3

source_name: Control Ab with IL-13

tag: NHBE cells treated with Control Ab with IL-13


title: IL-13 vs. Control 2

tag: NHBE cells treated with IL-13


title: Anti EGFR Ab and IL-13 vs. Control 3


title: IL-13 vs. Control 1


title: Benzoate 3rdBncy3Pycy5

city: Vancouver

first: Michael

last: McLeod

state: British Columbia

address: 4506 - 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

description: benzoate vs. pyruvate

data_processing: Normalized log ratio of means after background subtraction (CH1-BG1)/(CH2-BG2)

organism: Rhodococcus jostii RHA1

source_name: experiment

tag: experiment

source_name: control

tag: control


title: Biphenyl 3rdBicy3Pycy5

description: biphenyl vs. pyruvate


title: Ethylbenzene 3rdEtcy3Pycy5

description: ehtylbenze vs. pyruvate


title: Benzoate 2ndBncy5Pycy3

description: benzoate vs. pyruvate


title: Anti EGFR Ab No IL-13 vs. Control 2


title: Transcriptional response of E. coli to TPEN (t1)

first: Tara

last: Sigdel

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

description: DNA microarray slides were scanned by using the Genepix® 4000B Microarray scanner. Image analyses of scanned microarrays were performed using GenePix® Pro 5.0. (Axon). Images were visually inspected and spots affected by irregularities were flagged manually. Resulting data were filtered according to the following criteria: (a) removal of flagged spots (b) removal of spots with diameter <70 μm (average spot size on arrays is 120 μm), and (c) removal of spots with (% pixels 532 nm > background + 1 standard deviation) + (% pixels 635 nm > background + 1 standard deviation) < 100. For the remaining values, log2 transformations were applied, and linear normalizations were used to correct the parameter “median of ratios” to median = 0. For each series a two-tailed t-test was performed on the data from one dye combination (e.g. control cDNA were labeled Cy5 and cDNA from the TPEN stressed cells were labeled Cy3) and the corresponding dye-swap experiments (e.g. control cDNA were labeled Cy3 and and cDNA from the TPEN stressed cells were labeled Cy5).

data_processing: As described in the description

organism: Escherichia coli

source_name: E. coli K12 grown in minimal medium with added 5 μM TPEN

tag: mRNA

source_name: E. coli K12 grown in minimal medium without added TPEN


title: Ethylbenzene 2ndEtcy3Pycy5

description: ehtylbenze vs. pyruvate


title: Biphenyl 1stBicy5Pycy3

description: biphenyl vs. pyruvate


title: Transcriptional response of E. coli to TPEN (t2)

description: DNA microarray slides were scanned by using the Genepix? 4000B Microarray scanner. Image analyses of scanned microarrays were performed using GenePix? Pro 5.0. (Axon). Images were visually inspected and spots affected by irregularities were flagged manually. Resulting data were filtered according to the following criteria: (a) removal of flagged spots (b) removal of spots with diameter <70 μm (average spot size on arrays is 120 μm), and (c) removal of spots with (% pixels 532 nm > background + 1 standard deviation) + (% pixels 635 nm > background + 1 standard deviation) < 100. For the remaining values, log2 transformations were applied, and linear normalizations were used to correct the parameter ?median of ratios? to median = 0. For each series a two-tailed t-test was performed on the data from one dye combination (e.g. control cDNA were labeled Cy5 and cDNA from the TPEN stressed cells were labeled Cy3) and the corresponding dye-swap experiments (e.g. control cDNA were labeled Cy3 and and cDNA from the TPEN stressed cells were labeled Cy5).


title: Transcriptional response of E. coli to TPEN (t3)


title: Anti EGFR Ab No IL-13 vs. Control 1


title: Transcriptional response of E. coli to TPEN (m3)

data_processing: As described in description


title: W7(W7+Ca) Vs. W7+La(W7-Ca) - replica 3

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

description: Total RNA was extracted from seedling treated for one hour as decribed in the channels Characteristics. Hybridization was performed on an array from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K Arabidopsis ESTs. Data in this platform contains 3 repetitions of 3 independent biological experiments.

data_processing: Per spot and per chip: intensity dependent (lowess) normalization Genespring version GX 7.3.1

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings pretreated with La and treated with W7 (W7-Ca)

tag: Twelve-day old Arabidopsis seedlings were pretreated for 10 minutes with 0.35mM LaCl3 and treated with 0.6mM W7 (W7-Ca) for 1 hour

source_name: Arabidopsis seedlings treated with W7 (W7+Ca)

tag: Twelve-day old Arabidopsis seedlings were treated with 0.6 mM W7 (W7+Ca) for 1 hour.


title: Biphenyl 2ndBicy5Pycy3

description: biphenyl vs. pyruvate


title: W7+La(W7-Ca) Vs. DMSO+La(control) - replica 2

source_name: Arabidopsis seedlings pretreated with La and treated with DMSO (control)

tag: Twelve-day old Arabidopsis seedlings were pretreated for 10 minutes with 0.35mM LaCl3 and treated with 0.1% DMSO as control for 1 hour.

source_name: Arabidopsis seedlings treated with W7+La (W7-Ca)

tag: Twelve-day old Arabidopsis seedlings were pretreated for 10 minutes with 0.35mM LaCl3 and treated with 0.6mM W7 (W7-Ca) for 1 hour.


title: Ethylbenzene 1stEtcy5Pycy3

description: ehtylbenze vs. pyruvate


title: Benzoate 1stBncy5Pycy3

description: benzoate vs. pyruvate


title: Transcriptional response of E. coli to TPEN (m1)


title: W7(W7+Ca) Vs. W7+La(W7-Ca) - replica 1

data_processing: Per spot and per chip: intensity dependent (lowess) normailzation Genespring version GX 7.3.1

source_name: Arabidopsis seedlings pretreated with La, and treated with W7 (W7-Ca)


title: W7(W7+Ca) Vs. W7+La(W7-Ca) - replica 2


title: W7 Vs. DMSO(control) - replica 3

source_name: Arabidopsis seedlings treated with DMSO as control

tag: Twelve-day old Arabidopsis seedlings treated with 0.1% DMSO (control) for 1 hour.

source_name: Arabidopsis seedlings treated with W7

tag: Twelve-day old Arabidopsis seedlings were treated with 0.6 mM W7 (dissolved in 0.1% DMSO) for 1 hour.


title: W7 Vs. DMSO(control) - replica 2


title: HaCaT_4 hours_EMF exposure_S11_UE/UV

status: Public on Oct 12 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: We applied loop design for our microarray experiments in order to reduce the systemic error.

hyb_protocol: Microarray was first blocked by 0.1 mg/ml BSA, 3xSSC, and 0.1% SDS mixed solution for 1 hours at 50 oC. Then dipped in ddH2O for four times. Labeled cDNA was pipetted onto the center of the microarray and a coverslip (large enough to cover the entire array surface) was placed over the probe. The microarray was transferred in a hybridization chamber and four 16μl drops of 3x SSC were pipetted around the slide to provide humidity in the hybridization chamber (Takara, Japan). Then, the hybridization chamber was submerged in a 65℃ water bath for 16 to 20 hours. After hybridization was complete, the microarray was washed in 2x SSC and 0.1% SDS at 42°C for 5 min, followed by additional 10 min wash steps in 0.1x SSC and 0.1% SDS, 1mim in 0.1x SSC for four times, and 10s in 0.01 x SSC, each at room temperature.

scan_protocol: barcode=12766837 "PMTGain=595	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.15" Temperature=29.79 "ScanPower=100	100"

data_processing: Data processing will be described in detail in our website http://140.114.106.30/publication/tjweng/

source_name: Cells exposed to 5J/m2 UVB follow by 15G ELF-EMF for 4hours

label_protocol: 90μg total RNA and 7.34ng spike RNA was annealed to oligo(dT) and reversely transcribed by Superscript II (Invitrogen, Carlsbad, CA) to single strand cDNA labeled with Cy5-labeled dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Reactions were terminated using 0.1 N NaOH and then neutralized by 0.1 N HCl. Labeled cDNA was purified by microcon YM-30 column (Qiagen, Inc., Valencia, CA) and blocked by adding 20μg of Cot1 human DNA (Invitrogen, Carlsbad, CA), 20μg ployA RNA (Invitrogen, Carlsbad, CA) and 20μg tRNA (Invitrogen, Carlsbad, CA).

growth_protocol: Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100μg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone). Cells were routinely split 1: 6 every 3 days and have a plating efficiency of approximately 10%. For microarray experiments, 2×106 cells were seed 48 hours before treatment.

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 1.5 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

treatment_protocol: Cells exposed to 5J/m2 UVB follow by15G ELF-EMF for 4hours

tag: Cell line, Gender

value: male, Tissue:arm keratinocyte

source_name: Cells exposed to 5J/m2 UVB

label_protocol: 90μg total RNA and 7.34ng spike RNA was annealed to oligo(dT) and reversely transcribed by Superscript II (Invitrogen, Carlsbad, CA) to single strand cDNA labeled with Cy3-labeled dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Reactions were terminated using 0.1 N NaOH and then neutralized by 0.1 N HCl. Labeled cDNA was purified by microcon YM-30 column (Qiagen, Inc., Valencia, CA) and blocked by adding 20μg of Cot1 human DNA (Invitrogen, Carlsbad, CA), 20μg ployA RNA (Invitrogen, Carlsbad, CA) and 20μg tRNA (Invitrogen, Carlsbad, CA).

treatment_protocol: NoCells exposed to 5J/m2 UVB


title: Transcriptional response of E. coli to TPEN (m2)


title: W7 Vs. DMSO(control) - replica 1


title: HaCaT_4 hours_EMF exposure_S4_UV/UE

scan_protocol: barcode=12766766 "PMTGain=615	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.95	3.1" Temperature=27.83 "ScanPower=100	100"

label_protocol: 60μg total RNA and 4.96ng spike RNA was annealed to oligo(dT) and reversely transcribed by Superscript II (Invitrogen, Carlsbad, CA) to single strand cDNA labeled with Cy5-labeled dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Reactions were terminated using 0.1 N NaOH and then neutralized by 0.1 N HCl. Labeled cDNA was purified by microcon YM-30 column (Qiagen, Inc., Valencia, CA) and blocked by adding 20μg of Cot1 human DNA (Invitrogen, Carlsbad, CA), 20μg ployA RNA (Invitrogen, Carlsbad, CA) and 20μg tRNA (Invitrogen, Carlsbad, CA).

treatment_protocol: Cells exposed to 5J/m2 UVB

label_protocol: 60μg total RNA and 4.96ng spike RNA was annealed to oligo(dT) and reversely transcribed by Superscript II (Invitrogen, Carlsbad, CA) to single strand cDNA labeled with Cy3-labeled dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Reactions were terminated using 0.1 N NaOH and then neutralized by 0.1 N HCl. Labeled cDNA was purified by microcon YM-30 column (Qiagen, Inc., Valencia, CA) and blocked by adding 20μg of Cot1 human DNA (Invitrogen, Carlsbad, CA), 20μg ployA RNA (Invitrogen, Carlsbad, CA) and 20μg tRNA (Invitrogen, Carlsbad, CA).

treatment_protocol: Cells exposed to 5J/m2 UVB follow by 15G ELF-EMF for 4hours


title: HaCaT_4 hours_EMF exposure_S3_UE/EMF

scan_protocol: barcode=12767242 "PMTGain=620	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.88	3.14" Temperature=29.79 "ScanPower=100	100"

source_name: Cells exposed to 15G ELF-EMF for 4 hours


title: TFP Vs. DMSO(control) - replica 3

source_name: Arabidopsis seedlings treated with TFP

tag: Twelve-day old Arabidopsis seedlings were treated with 0.15 mM TFP (dissolved in 0.1% DMSO) for 1 hour.


title: W7+La(W7-Ca) Vs. DMSO+La(control) - replica 1

data_processing: Per spot and per chip: intensity dependent (lowess)normalization Genespring version GX 7.3.1

source_name: Arabidopsis seedlings treated with DMSO as control, pre treated with La3+

tag: Twelve-day old Arabidopsis seedlings pretreated with 0.35M LaCl3 for 10 minutes were treated with 0.1% DMSO (control) for 1 hour.

source_name: Arabidopsis seedlings treated with W7, pretreated with La3+ (W7-Ca)

tag: Twelve-day old Arabidopsis seedlings pretreated with 0.35M LaCl3 for 10 minutes were treated with 0.6 mM W7 (dissolved in 0.1% DMSO) for 1 hour.


title: W7+La(W7-Ca) Vs. DMSO+La(control) - replica 3

source_name: Arabidopsis seedlings treated with W7, pre treated with La3+ (W7-Ca)


title: TFP Vs. DMSO(control) - replica 2


title: Yeast FAIRE_BY4741 #1_Oligo Array Rando1

status: Public on Aug 11 2006

type: genomic

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

description: FAIRE_BY4741 #1_Oligo Array Rando1

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: The median of ratios data were obtained from Genepix GPR file. The log2 ratios were calculated from these data then block normalized to control for geographic variation across each array. Dye swap experiments were inverted.

molecule: genomic DNA

source_name: genomic unfixed BY4741

label_protocol: samples and references were amplified using a random primed PCR-based method (see Bohlander et al., 1992)

tag: genomic unfixed BY4741

source_name: fixed BY4741 #1

tag: fixed BY4741 #1


title: Yeast FAIRE_BY4741 #3_Oligo Array Rando5

description: FAIRE_BY4741 #3_Oligo Array Rando5

source_name: fixed BY4741 #3

tag: fixed BY4741 #3


title: 1-2 hour

source_name: 1-2 hour embryos

source_name: reference set


title: HaCaT_4 hours_EMF exposure_S7_UV/EMF

scan_protocol: barcode=12755907 "PMTGain=620	500" Scanner=GenePix 4100A 01  [100641] "LaserPower=2.95	3.12" Temperature=28.81 "ScanPower=100	100"

source_name: Cells exposed to 15G ELF-EMF for 4hours

treatment_protocol: Cells exposed to 15G ELF-EMF for 4hours


title: TFP Vs. DMSO(control) - replica 1


title: HaCaT_4 hours_EMF exposure_S5_EMF/UV

scan_protocol: barcode=12755902 "PMTGain=545	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.94	3.11" Temperature=29.3 "ScanPower=100	100"


title: HaCaT_4 hours_EMF exposure_S10_UE/Ctrl

scan_protocol: barcode=12766502 "PMTGain=560	510" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.89	3.09" Temperature=29.79 "ScanPower=100	100"

source_name: Control samples

treatment_protocol: No


title: HaCaT_4 hours_EMF exposure_S6_EMF/EMF

scan_protocol: barcode=12755904 "PMTGain=560	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.92	3.13" Temperature=29.3 "ScanPower=100	100"


title: HaCaT_4 hours_EMF exposure_S8_EMF/UE

scan_protocol: barcode=12767245 "PMTGain=630	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.96	3.12" Temperature=28.32 "ScanPower=100	100"

treatment_protocol: Cells exposed to 15G ELF-EMF for 4 hours


title: H.influenzae_110-1

status: Public on Jul 28 2006

city: Oklahoma City

first: Timothy

middle: M

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description: Biological replicate 1, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

hyb_protocol: Arrays were pre-hybridized in NimbleGen hybridization chamber at 45°C for two hours with gentle rotation using a buffer containing 100mg/ml herring sperm DNA (Promega Corporation, Madison, WI) 50mM MES, 1M NaCl, 10mM EDTA, 0.005% Tween-20 for fifteen minutes. The prehybe solution was replaced with a 350ml volume of the same composition as the pre-hybridization buffer but supplemented with 4mg of labeled prokaryotic cDNA and 1nM labeled control oligonucleotide. The array was hybridized overnight at 45°C with gentle rotation. Following hybridization, the arrays were removed from the hybridization and washed three times, at room temperature, in a buffer containing 6X SSPE, 0.01% (v/v) Tween-20 and then six times in a buffer containing 100mM MES, 26mM NaCl, 0.01% (v/v) Tween-20 at 45°C. Arrays were stained) in a buffer containing 50mM MES, pH 6.6, 1M NaCl, 0.005% Tween-20, and 1:1000 dilution of Streptavidin-Cy3 (GE Healthcare) for ten minutes with gentle agitation, then washed twice in 6X SSPE, 0.01% (v/v) Tween-20 at room temperature, dried under argon and stored desiccated.

scan_protocol: not provided

data_processing: RMA normalized using quantile normalization and gene calls generated using the RMA algorithm

organism: Haemophilus influenzae Rd KW20

source_name: H. influenzae Rd KW20 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 1

label_protocol: Total prokaryotic RNA is converted to cDNA by random primed reverse transcription with SuperScript II (Invitrogen Corporation, Carlsbad, CA) in a reaction containing 10mg RNA, 1mg random hexamer, 1200U SuperScript II, 1X SuperScript first strand buffer, 20mM DTT, 500mM dNTPs in a total volume of 60ml. Following incubation, residual RNA was enzymatically degraded with the addition of 1U RNase H and 1mg RNase A. Reactions were purified by extraction with phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation.in the presence of 1ml of Pellet Paint Co-Precipitant (EMD Biosciences, Madison WI). cDNA was enzymatically fragmented with 0.2U Dnase I in a 40ml reaction volume for 15 minutes at 37°C. Dnase I was inactivated by incubation at 99°C for ten minutes. Fragmented cDNA was end-labeled by the catalytic addition of 3’ biotin-N6-ddATP (Perkin-Elmer, Boston, MA) with terminal deoxynucleotidyl transferase (Promega Corporation, Madison, WI). The biotin-labeled reaction products were purified by centrifugal concentration through a Centricon YM-10 Concentrator (Millipore Corporation, Billerica, MA).

growth_protocol: H. influenzae Rd KW20 was used to inoculate 5 ml of brain heart infusion broth (BHI) containing 10ug/ml NAD and 0.1ug/ml hemin. These cultures were grown at 37C for 3 hours, collected by centrifugation, washed once in PBS with 0.1% gelatin, and resuspended in PBS-gelatin. The cultures were adjusted to an OD(605)=0.5. 5 ml of the cultures were inoculated into 60 ml of BHI broth containing NAD and 150uM deferoxamine to a final concentration of ~2x10^7 cfu/ml. 20 ml samples were taken after 90 minutes growth and transfered into an equal volume of RNAProtect reagent. Iron (500 uM FeCl3) and hemin (10ug/ml) were added to the remaining 40 ml and the cultures allowed to continue incubation at 37C for an additional 20 minutes post supplementation and 20 ml samples collected as above.

extract_protocol: RNA was prepared using Trizol (as described by the manufacturer). Residual genomic DNA was removed by treatment with RNase-free DNase (Invitrogen) as directed by the manufacturer and confirmed by q-rt-PCR analysis. RNA samples were then precipitated using LiCl and samples resolved by PAGE to ensure sample integrity.

tag: Strain Rd KW20


title: H.influenzae_110-2

description: Biological replicate 2, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

source_name: H. influenzae Rd KW20 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 2


title: Yeast FAIRE_BY4741 #3_Oligo Array Rando3 (dye swap)


title: HaCaT_4 hours_EMF exposure_S2_EMF/Ctrl

scan_protocol: barcode=12755906 "PMTGain=550	470" Scanner=GenePix 4100A 01  [100641] "LaserPower=2.98	3.13" Temperature=30.27 "ScanPower=100	100"


title: H.influenzae_90-2

description: Biological replicate 2, 90 minutes in FeHm Deplete BHI

source_name: H. influenzae Rd KW20 grown in iron and heme deplete media for 90 minutes, replicate 2


title: HaCaT_4 hours_EMF exposure_S9_Ctrl/UV

scan_protocol: barcode=12766764 "PMTGain=600	500" Scanner=GenePix 4100A 01  [100641] "LaserPower=3.04	3.05" Temperature=27.34 "ScanPower=100	100"


title: H.influenzae_90-3

description: Biological replicate 3, 90 minutes in FeHm Deplete BHI

source_name: H. influenzae Rd KW20 grown in iron and heme deplete media for 90 minutes, replicate 3


title: KG-1 treated with various Cordyceps sinensis extract_S15_QCS2/TW

status: Public on Jul 26 2006

hyb_protocol: 3 DNA array 50 kit protocol (Genisphere)

scan_protocol: Barcode=12606768 "PMTGain=750	580" Scanner=GenePix 4000B [81963] "LaserPower=3.51	4.47" Temperature=26.08 "ScanPower=33	33"

data_processing: Data processing will be described in detail in our website http://140.114.106.30/publication/mltsai/

source_name: KG-1 treated with QCS2 extract 20μl/ml, 4 days

growth_protocol: Fresh medium and Cordeceps extracts were replaced at day 2 after seeding. Cells were harvested at day 4 .

extract_protocol: Total RNA was isolated using Trizol reagent and purified by RNeasy . The quality of RNA was examined by capillary electrophoresis (Agilent chip).

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai intact Cordyceps sinensis(QCS) water extracts. In order to evaluate the quality of microarray result, duplicated QCS extract-treated samples, denoted as QCS-1 and QCS-2, were included as internal control samples.

tag: Cell line:

tag: KG-1 is a human CD34+ hemotopoietic progenitor cell line that has been used as an in vitro cell model system for the study of dendritic cells .

tag: TCM:

tag: Cordyceps sinensis, a parasitic fungus, infects the caterpillar larva of the moth Hepilus fabricius.It is a well-known nutritious tonic and one of the most valuable Chinese herbal medicines.

source_name: KG-1 treated with TW extract 20μl/ml, 4 days

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Tibet host worm Cordyceps sinensis (TW) water extracts.


title: KG-1 treated with various Cordyceps sinensis extract_S13_QCS1/TFB

scan_protocol: Barcode=12605194 "PMTGain=750	580" Scanner=GenePix 4000B [81963] "LaserPower=3.33	4.25" Temperature=23.34 "ScanPower=33	33"

source_name: KG-1 treated with QCS1 extract 20μl/ml, 4 days

label_protocol: 3 DNA array 50 kit protocol (Genisphere)

source_name: KG-1 treated with TFB extract 20μl/ml, 4 days

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Tibet fruiting body Cordyceps sinensis(TFB) water extracts.


title: KG-1 treated with various Cordyceps sinensis extract_S14_TW/QCS1

scan_protocol: Barcode=12587859 "PMTGain=750	600" Scanner=GenePix 4000B [84942] "LaserPower=2.86	3.28" Temperature=28.01 "ScanPower=33	33"

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Tibet host worm Cordyceps sinensis(TW) water extracts.


title: KG-1 treated with various Cordyceps sinensis extract_S8_QFB/Control

scan_protocol: Barcode=12605505 "PMTGain=750	540" Scanner=GenePix 4000B [81963] "LaserPower=3.23	4.51" Temperature=26.2 "ScanPower=33	33"

source_name: KG-1 treated with QFB extract 20μl/ml, 4 days

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai fruiting body Cordyceps sinensis (QFB) water extracts.

source_name: KG-1 without treatment (control), 4 days

growth_protocol: Fresh medium were replaced at day 2 after seeding. Cells were harvested at day 4 .


title: KG-1 treated with various Cordyceps sinensis extract_S12_TFB/Control

scan_protocol: Barcode=12584063 "PMTGain=750	600" Scanner=GenePix 4000B [84942] "LaserPower=2.91	3.21" Temperature=27.79 "ScanPower=33	33"

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Tibet fruiting body Cordyceps sinensis (TFB) water extracts.

treatment_protocol: The KG-1 cells without treatment (control) .


title: KG-1 treated with various Cordyceps sinensis extract_S11_Control/QW

scan_protocol: Barcode=12584061 "PMTGain=710	600" Scanner=GenePix 4000B [84942] "LaserPower=2.93	3.66" Temperature=30.94 "ScanPower=100	33"

source_name: KG-1 treated with QW extract 20μl/ml, 4 days

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai host worm Cordyceps sinensis (QW) water extracts.


title: KG-1 treated with various Cordyceps sinensis extract_S10_QW/TCS

scan_protocol: Barcode=12606766 "PMTGain=730	600" Scanner=GenePix 4000B [81963] "LaserPower=3.76	4.39" Temperature=32.43 "ScanPower=33	33"

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai host worm Cordyceps sinensis(QW) water extracts.

source_name: KG-1 treated with TCS extract 20μl/ml, 4 days

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Tibet intact Cordyceps sinensis(TCS) water extracts.


title: KG-1 treated with various Cordyceps sinensis extract_S6_TW/TCS

scan_protocol: Barcode=12605356 "PMTGain=750	550" Scanner=GenePix 4000B [81963] "LaserPower=3.09	4.24" Temperature=24.5 "ScanPower=33	33"


title: KG-1 treated with various Cordyceps sinensis extract_S16_ QFB/QCS2

scan_protocol: Barcode=12587860 "PMTGain=750	600" Scanner=GenePix 4000B [84942] "LaserPower=2.9	3.21" Temperature=29.5 "ScanPower=33	33"

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai fruiting body Cordyceps sinensis(QFB) water extracts.


title: KG-1 treated with various Cordyceps sinensis extract_S7_Control/TW

scan_protocol: Barcode=12605504 "PMTGain=730	530" Scanner=GenePix 4000B [81963] "LaserPower=3.22	4.54" Temperature=25.59 "ScanPower=33	33"

treatment_protocol: The KG-1 cells without treatment (control)


title: KG-1 treated with various Cordyceps sinensis extract_S4_TFB/QCS2

scan_protocol: Barcode=12605353 "PMTGain=790	500" Scanner=GenePix 4000B [81963] "LaserPower=3.41	4.53" Temperature=28.07 "ScanPower=33	33"

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai intact Cordyceps sinensis(QCS2) water extracts. In order to evaluate the quality of microarray result, duplicated QCS extract-treated samples, denoted as QCS-1 and QCS-2, were included as internal control samples.


title: Flow sorted derivative chromosomes from Case 2 t(2;7) Ref 397796

city: Hinxton

first: Nigel

middle: Paul

last: Carter

state: Cambirdge

address: Wellcome Trust Genome Campus

department: Molecular Cytogenetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: flow sorted derivative chromosomes

data_processing: un-normalised raw intensities with no background subtraction and linear ratios (derivative 2/derivative 7)

source_name: derivative 2

tag: derivative 2

source_name: derivative 7

tag: derivative 7


title: KG-1 treated with various Cordyceps sinensis extract_S3_QCS2/QW

scan_protocol: Barcode=12605198 "PMTGain=800	500" Scanner=GenePix 4000B [81963] "LaserPower=3.32	4.52" Temperature=27.46 "ScanPower=33	33"


title: KG-1 treated with various Cordyceps sinensis extract_S9_TCS/QFB

scan_protocol: Barcode=12606763 "PMTGain=740	600" Scanner=GenePix 4000B [81963] "LaserPower=3.81	4.33" Temperature=33.41 "ScanPower=33	33"


title: KG-1 treated with various Cordyceps sinensis extract_S5_TCS/TFB

scan_protocol: Barcode=12605354 "PMTGain=750	530" Scanner=GenePix 4000B [81963] "LaserPower=3.03	4.31" Temperature=23.12 "ScanPower=33	33"


title: Slide 1 wt vs glna

status: Public on Jun 24 2006

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: For experimental protocols see: Kloosterman et al. 2006. REGULATION OF GLUTAMINE AND GLUTAMATE METABOLISM BY GLNR AND GLNA IN STREPTOCOCCUS PNEUMONIAE.

data_processing: MicroPreP (PMID: 15907200)

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae wild-type

tag: Streptococcus pneumoniae wild-type

source_name: Streptococcus pneumoniae glnA KO

tag: Streptococcus pneumoniae glnA KO


title: Slide 1 wt vs glnr

source_name: Streptococcus pneumoniae glnR KO

tag: Streptococcus pneumoniae glnR KO


title: Slide 2 glna vs wt


title: Slide 2 glnr vs wt


title: Flow sorted derivative chromosomes from Case 4 t(11;17) Ref 41581

description: flow sorted derivative chromosomes


title: Slide 3 wt vs glna


title: Flow sorted derivative chromosomes from Case 3 t(2;7) Ref 46070

description: flow sorted derivative chromosomes


title: H.influenzae_110-3

description: Biological replicate 3, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

scan_protocol: not provided

source_name: H. influenzae Rd KW20 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 3


title: Flow sorted derivative chromosomes from Case 1 t(2;7) Ref 34778

description: flow sorted derivative chromosomes


title: KG-1 treated with various Cordyceps sinensis extract_S2_QW/ QCS1

scan_protocol: Barcode=12605196 "PMTGain=780	500" Scanner=GenePix 4000B [81963] "LaserPower=3.27	4.53" Temperature=26.66 "ScanPower=33	33"

treatment_protocol: The KG-1 cells were treated with 20μl/ml of Qinghai intact Cordyceps sinensis(QCS1) water extracts. In order to evaluate the quality of microarray result, duplicated QCS extract-treated samples, denoted as QCS-1 and QCS-2, were included as internal control samples.


title: Slide 3 glnr vs wt


title: Serum response of fibroblasts 20 hr.

status: Public on Dec 31 2005

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12605.gif
Measurement: time(absolute) 20 h
name: 12605_Time

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

source_name: Pool of timepoints and unsync. cells

tag: Pool of timepoints and unsync. cells

source_name: Fibroblasts 20 hr.

tag: Fibroblasts 20 hr.


title: Serum response of fibroblasts 15 min.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12193.gif
Measurement: time(absolute) 0.25 h
name: 12193_Time

source_name: Fibroblasts 15 min.

tag: Fibroblasts 15 min.


title: Serum response of fibroblasts 36 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12610.gif
Measurement: time(absolute) 36 h
name: 12610_Time

source_name: Fibroblasts 36 hr.

tag: Fibroblasts 36 hr.


title: Serum response of fibroblasts 0 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12190.gif
Measurement: time(absolute) 0 h
name: 12190_Time

source_name: Fibroblasts 0 hr.

tag: Fibroblasts 0 hr.


title: Serum response of fibroblasts 4 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12587.gif
Measurement: time(absolute) 4 h
name: 12587_Time

source_name: Fibroblasts 4 hr.

tag: Fibroblasts 4 hr.


title: H.influenzae_90-1

description: Biological replicate 1, 90 minutes in FeHm deplete BHI

source_name: H. influenzae Rd KW20 grown in iron and heme deplete media for 90 minutes, replicate 1


title: Serum response of fibroblasts 6 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12589.gif
Measurement: time(absolute) 6 h
name: 12589_Time

source_name: Fibroblasts 6 hr.

tag: Fibroblasts 6 hr.


title: Human Malaria __raw_ 4

status: Public on Jul 09 2005

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37537.gif

source_name: reference

tag: Stratagene, amplified with Ambion method

source_name: clinical sample

tag: 10_Malaria;  PAXgene sample


title: Serum response of fibroblasts 0 hr. (C)

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12613.gif
Measurement: time(absolute) 0 h
name: 12613_Time

source_name: Fibroblasts 0 hr. (C)

tag: Fibroblasts 0 hr. (C)


title: MCF7_DamID_CBX1V5EcoDam(Cy5)-EcoDam(Cy3)_55435_SeriesC

status: Public on Oct 17 2006

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. Raw data files were loaded in R. We did not apply a background correction to the data. DamID data were normalized within arrays (method=loess) and normalized between different arrays (method=Aquantile).

growth_protocol: MCF7 cells were maintained in DMEM medium supplemented with 10% FCS and antibiotics.

extract_protocol: For detailed protocols go to www.nki.nl/nkidep/vansteensel.

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MCF7 cells were transfected with Dam or Dam-fusion protein expressing constructs.  Cells were selected with G418 for stable integration of the constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR. NimbleGen labeled the samples with a fluorescent dye and hybridized them to microarrays.

tag: MCF7 human breast carcinoma cells expressing CBX1-V5-EcoDam fusion protein.

tag: MCF7 human breast carcinoma cells expressing EcoDam protein.


title: Serum response of fibroblasts 3 hr.

last: Stanford Microarray Database

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12586.gif
Measurement: time(absolute) 3 h
name: 12586_Time

source_name: Fibroblasts 3 hr.

tag: Fibroblasts 3 hr.


title: Serum response of fibroblasts 10 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12207.gif
Measurement: time(absolute) 10 h
name: 12207_Time

source_name: Fibroblasts 10 hr.

tag: Fibroblasts 10 hr.


title: Serum response of fibroblasts 2 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12579.gif
Measurement: time(absolute) 2 h
name: 12579_Time

source_name: Fibroblasts 2 hr.

tag: Fibroblasts 2 hr.


title: Serum response of fibroblasts 12 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12208.gif
Measurement: time(absolute) 12 h
name: 12208_Time

source_name: Fibroblasts 12 hr.

tag: Fibroblasts 12 hr.


title: Serum response of fibroblasts 16 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12593.gif
Measurement: time(absolute) 16 h
name: 12593_Time

source_name: Fibroblasts 16 hr.

tag: Fibroblasts 16 hr.


title: MCF7_DamID_CBX1V5EcoDam(Cy3)-EcoDam(Cy5)_60360_SeriesD


title: Yeast FAIRE_BY4741 #2_Oligo Array Rando4 (dye swap)

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

source_name: fixed BY4741 #2

tag: fixed BY4741 #2

source_name: genomic unfixed BY4741

tag: genomic unfixed BY4741


title: Human Malaria __raw_27

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37528.gif

tag: 9_Malaria;  PAXgene sample


title: Human Malaria __raw_20

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37529.gif

tag: 19_Lower respiratory tract infection ;  PAXgene sample


title: Serum response of fibroblasts 8 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12590.gif
Measurement: time(absolute) 8 h
name: 12590_Time

source_name: Pool of timepoints and unsync. cells

tag: Pool of timepoints and unsync. cells

source_name: Fibroblasts 8 hr.

tag: Fibroblasts 8 hr.


title: Serum response of fibroblasts 24 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12609.gif
Measurement: time(absolute) 24 h
name: 12609_Time

source_name: Fibroblasts 24 hr.

tag: Fibroblasts 24 hr.


title: Serum response of fibroblasts 1 hr.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12202.gif
Measurement: time(absolute) 1 h
name: 12202_Time

source_name: Fibroblasts 1 hr.

tag: Fibroblasts 1 hr.


title: Serum response of fibroblasts 30 min.

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12197.gif
Measurement: time(absolute) 0.5 h
name: 12197_Time

source_name: Fibroblasts 30 min.

tag: Fibroblasts 30 min.


title: Human Malaria __raw_19

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37536.gif

tag: Stratagene, amplified with Ambion method

tag: 15_Malaria;  PAXgene sample


title: Human Malaria __raw_ 1

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37534.gif

tag: 24_Malaria;  PAXgene sample


title: Human Malaria __raw_ 6

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37519.gif

tag: 16_Malaria;  PAXgene sample


title: Human Malaria __raw_ 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37535.gif

tag: 12_Malaria;  PAXgene sample


title: Human Malaria __raw_12

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37517.gif

tag: 2_Convalescent, follow-up to #12;  PAXgene sample


title: Human Malaria __raw_15

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37526.gif

tag: 8_Convalescent, follow-up to #16;  PAXgene sample


title: Human Malaria __raw_13

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37518.gif

tag: 4_Convalescent, follow-up to #10;  PAXgene sample


title: 03_EML

status: Public on Jun 01 2004

city: Aurora

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

description: 'usual' emphysemic lung

source_name: lung tissue


title: 04_EML

description: 'usual' emphysemic lung


title: Serum response of fibroblasts 1 1/2 hr.

city: Stanford

address: 300 Pasteur Drive

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12205.gif
Measurement: time(absolute) 1.5 h
name: 12205_Time

source_name: Fibroblasts 1 1/2 hr.

tag: Fibroblasts 1 1/2 hr.


title: 05_ADL

description: Alpha-1 Antitrypsin Deficiency-related emphysemic lung


title: 06_ADL


title: 03_ADL


title: 04_ADL


title: Human Malaria __raw_17

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37508.gif

source_name: reference

tag: 13_Malaria;  PAXgene sample


title: 02_ADL


title: 05_EML

description: 'usual' emphysemic lung


title: 01_EML

description: 'usual' emphysemic lung


title: Serum response of fibroblasts 0 hr. (B)

description:
Simple annotation: Serum-response, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12612.gif
Measurement: time(absolute) 0 h
name: 12612_Time

source_name: Fibroblasts 0 hr. (B)

tag: Fibroblasts 0 hr. (B)


title: Human Malaria __raw_26

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37509.gif

source_name: clinical sample

tag: 7_Pharyngeal Infection;  PAXgene sample


title: Human Malaria __raw_ 9

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37525.gif

tag: 11_Malaria;  PAXgene sample


title: Human Malaria __raw_29

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37516.gif

tag: 22_Malaria;  PAXgene sample


title: 05_NML

description: Normal lung


title: 02_EML

description: 'usual' emphysemic lung


title: Human Malaria __raw_23

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37511.gif

tag: 5_Febrile Fit;  PAXgene sample


title: Human Malaria __raw_31

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37510.gif

tag: 17_Malaria;  PAXgene sample


title: 04_NML

description: Normal lung


title: Human Malaria __raw_ 5

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37539.gif

tag: 26_Malaria;  PAXgene sample


title: Human Malaria __raw_10

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37512.gif

tag: Stratagene, amplified with Ambion method

tag: 1_Convalescent, follow-up to #11;  PAXgene sample


title: Human Malaria __raw_11

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37515.gif

tag: 6_Convalescent, follow-up to #24;  PAXgene sample


title: 03_NML

description: Normal lung


title: Human Malaria __raw_21

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37523.gif

tag: 14_Lower respiratory tract infection ;  PAXgene sample


title: Human Malaria __raw_ 8

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37507.gif

tag: 21_Malaria;  PAXgene sample


title: Human Malaria __raw_14

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37522.gif

tag: 3_Convalescent, follow-up to #23;  PAXgene sample


title: Human Malaria __raw_28

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37530.gif

tag: 20_Malaria;  PAXgene sample


title: 02_NML

description: Normal lung


title: 01_NML

description: Normal lung


title: Human Malaria __raw_30

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37506.gif

tag: 18_Malaria;  PAXgene sample


title: Human Malaria __raw_ 7

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37520.gif

tag: 23_Malaria;  PAXgene sample


title: Human Malaria __raw_18

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37538.gif

tag: 28_Sepis(Strp.Pneu.)/Malaria;  PAXgene sample


title: Human Malaria __raw_16

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37514.gif

tag: 27_Sepsis/Meningitis (Haem.Infl.);  PAXgene sample


title: Human Malaria __raw_22

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37531.gif

tag: 25_Sepsis(E.Coli);  PAXgene sample