title: 13688400 - Root Col0 set1 vs Meiocytes Col0 set1

hyb_protocol: Meiocytes Col0 set1 Cy5 / Root Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688042 - Root Col0 set2 vs Anther Col0 set2

status: Public on Dec 07 2008

type: other

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the gene expressed during meiosis pathway in Arabidopsis thalina.

hyb_protocol: Anther Col0 set2 Cy5 / Root Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: other

organism: Arabidopsis thaliana

source_name: Anther Col0 set2

label_protocol: labelling  , amplification=,   .

growth_protocol: stamen - Media=soil 	 hygrometry=70	 Temperature=18	 Light=11h

extract_protocol: Anther Col0 set2:1.56ug.

tag: Arabidopsis thaliana (col-0)  - harvest date:01-04-07

source_name: Root Col0 set2

growth_protocol: root - Media=soil 	 hygrometry=70	 Temperature=18	 Light=11h

extract_protocol: Root Col0 set2:168.17ug.

tag: Arabidopsis thaliana (col-0)  - harvest date:01-09-07


title: patient_18_a

status: Public on Oct 30 2008

type: RNA

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

country: USA

institute: Duke University Medical Center

description: In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1.  For patient #1, we had 3 lesions from the extremity region harboring the  melanoma disease.

hyb_protocol: labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method.  RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities.  Normalization was done using quantile normalization.  Expression values were then transformed by taking Logarithm base 2

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: melanoma

label_protocol: one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

extract_protocol: Tissue was homogenized and RNA isolated using Qiagen Rneasy kit.  A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue.  Each RNA isolation included treatment with Dnase to minimize genomic DNA.

treatment_protocol: Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch.  The samples were snap frozen and stored at -133°C until ready for further analysis.  All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.

tag: punch biopsy

tag: in-transit disease


title: patient_14_a


title: patient_15_c


title: patient_13_b


title: patient_17_a


title: patient_15_a


title: patient_14_b


title: patient_12_a


title: patient_13_c


title: patient_13_a


title: patient_11_c


title: patient_16_a


title: patient_15_b


title: patient_19_a


title: patient_19_b


title: patient_18_b


title: patient_16_c


title: patient_10_a


title: patient_12_c


title: patient_11_b


title: patient_16_b


title: patient_20_b


title: patient_11_a


title: patient_10_b


title: patient_6_b


title: patient_17_b


title: patient_20_a


title: 13688404 - Root Col0 set1 vs Anther Col0 set1

hyb_protocol: Anther Col0 set1 Cy5 / Root Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Anther Col0 set1

extract_protocol: Anther Col0 set1:22.2ug.

source_name: Root Col0 set1

extract_protocol: Root Col0 set1:77.54ug.


title: patient_4_d


title: patient_5_c


title: benomyl_80min CG

status: Public on Sep 01 2008

city: Paris

first: Gaëlle

last: Lelandais

address: 2, place Jussieu

institute: INSERM

description: Time = 80min

hyb_protocol: Complete protocol can be found online : http://www.transcriptome.ens.fr/sgdb/protocols/hybridisation_yeast.php

scan_protocol: The microarrays were read using a Genepix 4000B scanner (Axon) and analyzed with the Genepix 6.0 software.

data_processing: Artefactual and saturated signal spots were eliminated. After image quantification, data were normalized over all features with print-tip lowess using the R/BioConductor packages “limma” and “marray” available at http://www.bioconductor.org/.

organism: Nakaseomyces glabratus

source_name: Total RNA from benomyl treated cells labeled with Cyanine-5 (red).

label_protocol: Complete protocol can be found online : http://www.transcriptome.ens.fr/sgdb/protocols/labelling_yeast.php

growth_protocol: All experiments were conducted in YPD rich media (2% glucose, 1% bactopeptone, 1% yeast extract).

extract_protocol: Complete protocol can be found online : http://www.transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php

treatment_protocol: Cells were grown to OD600nm = 0.6 and then treated with benomyl (Sigma-Aldrich) to a final concentration of 20μg/ml (stock solution: 10 mg/ml in DMSO). The mock treatment was done with an equivalent volume of DMSO. The cells were snapped- frozen in cold ethanol (final concentration 70% at -80°C) after 2, 4, 10, 20, 40 and 80 minutes of benomyl or mock treatment.

tag: Strain BY4742, 80min after benomyl addition in growth media

source_name: Total RNA from mock treated cells labeled with Cyanine-3 (green).

tag: Strain BY4742, 80min after DMSO addition in growth media


title: benomyl_4min SC

description: Time = 4min

organism: Saccharomyces cerevisiae

tag: Strain BY4742, 4min after benomyl addition in growth media

tag: Strain BY4742, 4min after DMSO addition in growth media


title: benomyl_80min SC

description: Time = 80min


title: benomyl_20min SC

description: Time = 20min

tag: Strain BY4742, 20min after benomyl addition in growth media

tag: Strain BY4742, 20min after DMSO addition in growth media


title: patient_5_b


title: benomyl_2min SC

description: Time = 2min

tag: Strain BY4742, 2min after benomyl addition in growth media

source_name: Total RNA from mock (DMSO) treated cells labeled with Cyanine-3 (green).

tag: Strain BY4742, 2min after DMSO addition in growth media


title: patient_4_c


title: benomyl_40min SC

description: Time = 40min

tag: Strain BY4742, 40min after benomyl addition in growth media

tag: Strain BY4742, 40min after DMSO addition in growth media


title: benomyl_10min SC

description: Time = 10min

tag: Strain BY4742, 10min after benomyl addition in growth media

tag: Strain BY4742, 10min after DMSO addition in growth media


title: patient_3_c


title: patient_6_a


title: patient_4_b


title: patient_4_a


title: patient_5_a


title: patient_2_b


title: patient_3_a


title: patient_2_a


title: benomyl_4min CG

description: Time = 4min


title: benomyl_40min CG

description: Time = 40min


title: benomyl_20min CG

description: Time = 20min


title: patient_3_b


title: benomyl_2min CG

description: Time = 2min


title: Series 1, Sample OC08

status: Public on Jul 31 2008

city: Charlotte

first: Zahra

middle: Bahrani

last: Mostafavi

address: 1542 Garden Terrece

department: Research

institute: Carolinas Medical Center

description: Gene expression analysis of Ovarian Tissue Sample. RNA from each ovary was extracted and hybridized on a microarray.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite Version 5.0

label: Biotin

source_name: Malignant Human Ovary

label_protocol: Standard Affymetrix procedures

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, San Diego, CA) according to manufacturer recommendations. The product from the initial extraction was then further purified using the RNeasy Mini Kit (Qiagen, Valencia, CA). Sample quantity and purity was determined using the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene, OR). RNA integrity was confirmed using agarose gel electrophoresis.

tag: Malignant Human Ovary


title: benomyl_10min CG

description: Time = 10min


title: Series 1, Sample OC104


title: Series 1, Sample OC10v2

source_name: Benign Human Ovary

tag: Benign Human Ovary


title: Series 1, Sample OC128

source_name: Borderline Malignant Human Ovary

label_protocol: Standard Affymetrix Procedures

tag: Borderline Malignant Human Ovary


title: Series 1, Sample OC158


title: Series 1, Sample OC15


title: Series 1, Sample OC16

source_name: Normal Human Ovary

tag: Normal Human Ovary


title: Series 1, Sample OC157


title: Series 1, Sample OC11


title: Series 1, Sample OC14


title: Series 1, Sample OC136


title: Series 1, Sample OC134


title: Series 1, Sample OC169


title: Series 1, Sample OC164


title: Series 1, Sample OC123


title: Series 1, Sample OC159


title: Series 1, Sample OC167


title: Series 1, Sample OC127


title: Series 1, Sample OC173

description: Genetic Profiling of Ovarian Tissue Sample. RNA from each ovary was extracted and hybridized on a microarray.


title: Series 1, Sample OC17


title: Series 1, Sample OC174v2


title: Series 1, Sample OC166


title: Series 1, Sample OC132


title: Series 1, Sample OC18


title: Series 1, Sample OC180


title: Series 1, Sample OC187


title: Series 1, Sample OC184


title: Series 1, Sample OC179v2


title: Series 1, Sample OC19


title: Series 1, Sample OC190


title: Series 1, Sample OC117


title: Series 1, Sample OC28


title: Series 1, Sample OC200


title: Series 1, Sample OC20


title: Series 1, Sample OC209


title: Series 1, Sample OC27


title: Series 1, Sample OC47v2


title: Series 1, Sample OC193


title: Series 1, Sample OC50


title: Series 1, Sample OC54


title: Series 1, Sample OC62


title: Series 1, Sample OC29


title: Series 1, Sample OC34


title: Series 1, Sample OC51


title: Series 1, Sample OC44


title: Series 1, Sample OC61


title: Series 1, Sample OC52


title: Series 1, Sample OC65


title: Series 1, Sample OC48


title: Series 1, Sample OC49


title: Series 1, Sample OC56


title: Series 1, Sample OC33


title: Series 1, Sample OC207


title: Series 1, Sample OC201


title: Series 1, Sample OC60


title: Series 1, Sample OC68

tag: Borderline Human Ovary


title: Series 1, Sample OC66


title: Series 1, Sample OC71


title: Series 1, Sample OC72


title: Series 1, Sample OC79


title: Series 1, Sample HTB75v2


title: Series 1, Sample OC92


title: Series 1, Sample OC82


title: Ecoli_treated_cefmec_5min_rep2

status: Public on Jul 15 2008

city: University Park

first: Mary

middle: Elizabeth

last: Laubacher

state: PA

address: 317 S Frear

department: Biochemistry Microbiology and Molecular Biology

institute: Pennsylvania State University

description: Gene expression data from E. coli cells treated with 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam

hyb_protocol: Labeled cDNA was hybridized according to the Affymetrix manual for E. coli Antisense chips and were washed and stained in the GeneChip Fluids Station 400

scan_protocol: Chips were scanned with the GCS3000 scanner

data_processing: The data were analyzed with the robust multichip averaging (RMA) program in the Simpleaffy package for the Bioconductor statistics environment.  Genes with significant changes in gene expression were identified using the significance analysis of microarrays (SAM) program using two-way paired comparison with a false discovery rate of 0.958 % for cef/mec.

organism: Escherichia coli K-12

source_name: Treated E. coli 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam 5 minute

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual).

growth_protocol: Cultures of MG1655 were grown overnight at 37°C for 14-16 hours Cultures of SEA113 (MG1655) were grown in LB at 37°C overnight (14-18 hrs) with rotation.  The overnight cultures were diluted in fresh media to an OD600 of 0.02 and grown at 37°C with shaking in a gyrotary water bath until an OD600 of 0.2, at which point antibiotics were added.

extract_protocol: Samples were collected from both the treated and untreated cultures 5 minutes before treatment as well as 5, 20 and 40 minutes after treatment.  The 40 minute time point was immediately before cell growth slowed due to antibiotic treatment. 10 ml of culture was added to an ice-cold 5% phenol/ethanol solution to stop further transcription.  RNA was extracted using the hot phenol method of extraction.

treatment_protocol: Antibiotics were added to final concentration of 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam when the culture reached an OD of approximately 0.2.  In the case of the combination treatment the same concentrations were used but the antibiotics were measured and mixed prior to addition.


title: Series 1, Sample OC89


title: Ecoli_treated_cefmec_20min_rep3

source_name: Treated E. coli 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam 20 minute


title: Ecoli_treated_cefmec_5min_rep3


title: Ecoli_treated_cefmec_40min_rep1

source_name: Treated E. coli 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam 40 minute

tag: MG1655 rpoHP3::lacZ


title: Ecoli_treated_cefmec_5min_rep1


title: Ecoli_treated_cefmec_20min_rep1


title: Series 1, Sample HTB77v2


title: Ecoli_treated_cefmec_40min_rep4_1


title: Ecoli_treated_cefmec_40min_rep2


title: Ecoli_treated_cefmec_20min_rep2


title: Ecoli_treated_cefmec_40min_rep3


title: Ecoli_treated_cefmec_-5min_rep1

source_name: Treated E. coli 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam -5 minute


title: Ecoli_treated_mecillinam0.03_40min_rep2

description: Gene expression data from E. coli cells treated with 0.03 ug/ml mecillinam

source_name: Treated E. coli 0.03 ug/ml mecillinam 40 minute


title: Series 1, Sample OC04


title: Ecoli_treated_mecillinam0.03_40min_rep1


title: Ecoli_treated_mecillinam0.03_20min_rep1

source_name: Treated E. coli 0.03 ug/ml mecillinam 20 minute


title: Ecoli_treated_mecillinam0.03_5min_rep2

source_name: Treated E. coli 0.03 ug/ml mecillinam 5 minute


title: Ecoli_treated_mecillinam0.03_5min_rep1


title: Ecoli_treated_mecillinam0.03_20min_rep2


title: Series 1, Sample OC75


title: Ecoli_treated_cefmec_-5min_rep2


title: Ecoli_treated_mecillinam0.03_40min_rep3


title: Ecoli_treated_cefsulodin10_40min_rep3

description: Gene expression data from E. coli cells treated with 10 ug/ml cefsulodin

source_name: Treated E. coli 10 ug/ml cefsulodin 40 minute


title: Ecoli_treated_mecillinam0.03_-5min_rep1

source_name: Treated E. coli 0.03 ug/ml mecillinam -5 minute


title: Ecoli_treated_cefsulodin10_40min_rep2


title: Ecoli_treated_mecillinam0.03_-5min_rep2


title: Ecoli_treated_cefmec_-5min_rep3


title: Ecoli_treated_cefmec_40min_rep4_2

data_processing: The data were analyzed with the robust multichip averaging (RMA) program in the Simpleaffy package for the Bioconductor statistics environment.  Genes with significant changes in gene expression were identified using the significance analysis of microarrays (SAM) program using two-way paired comparison with false discovery rates of 0.828% for mecillinam and 1.67% for cefsulodin.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA except that the BioArrayTM terminal labeling kit (Enzo Life Sciences, Farmingdale, NY) was used to label the cDNA.  (Expression Analysis Technical Manual).

growth_protocol: Cultures of MG1655 were grown overnight at 37°C for 14-16 hours Cultures of SEA113 (MG1655) were grown in LB at 37°C overnight (14-18 hrs) with rotation.  The overnight cultures were diluted in fresh media to an OD600 of 0.02 and grown at 37°C with shaking in a gyratory water bath until an OD600 of 0.2, at which point antibiotics were added.

extract_protocol: Samples were collected from both the treated and untreated cultures at time points immediately before cell growth slowed due to antibiotic treatment (40 min. after treatment with a combination of cefsulodin and mecillinam, 10 min. after cefsulodin treatment, and 60 min. after mecillinam treatment), and added to an ice-cold 5% phenol/ethanol solution to stop further transcription.  RNA was extracted using the hot phenol method of extraction.

treatment_protocol: Antibiotics were added to the final concentrations of 60 ug/ml cefsulodin, 0.3 ug/ml mecillinam, or the combination of 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam when the culture reached an OD of approximately 0.2.


title: Ecoli_treated_cefsulodin10_20min_rep1

source_name: Treated E. coli 10 ug/ml cefsulodin 20 minute


title: Ecoli_treated_cefsulodin10_20min_rep2


title: Ecoli_treated_cefsulodin10_5min_rep1

source_name: Treated E. coli 10 ug/ml cefsulodin 5 minute


title: Ecoli_treated_cefsulodin10_-5min_rep1

source_name: Treated E. coli 10 ug/ml cefsulodin -5 minute


title: Ecoli_treated_cefsulodin10_40min_rep1


title: Ecoli_treated_mecillinam0.3_60min_rep3

description: Gene expression data from E. coli cells treated with 0.3 ug/ml mecillinam

source_name: Treated E. coli 0.3 ug/ml mecillinam 60 minute


title: Ecoli_treated_cefsulodin10_5min_rep2


title: Ecoli_treated_cefsulodin60_10min_rep3

description: Gene expression data from E. coli cells treated with 60 ug/ml cefsulodin

source_name: Treated E. coli 60 ug/ml cefsulodin 10 minute


title: Ecoli_untreated_40min_rep4_1

description: Gene expression data from untreated E. coli cells

source_name: Untreated E. coli 40 minute


title: Ecoli_treated_cefsulodin60_10min_rep1


title: Ecoli_treated_mecillinam0.3_60min_rep2


title: Ecoli_untreated_40min_rep3


title: Ecoli_treated_cefsulodin10_-5min_rep2


title: Ecoli_untreated_40min_rep1


title: Ecoli_untreated_40min_rep2


title: Ecoli_treated_cefsulodin60_20min_rep1

source_name: Treated E. coli 60 ug/ml cefsulodin 5 minute


title: Ecoli_treated_cefsulodin60_5min_rep1


title: Ecoli_untreated_40min_rep4_2


title: Ecoli_treated_mecillinam0.3_60min_rep1


title: Ecoli_treated_cefsulodin60_5min_rep2


title: Ecoli_untreated_5min_rep2

source_name: Untreated E. coli 5 minute


title: Ecoli_untreated_20min_rep1

source_name: Untreated E. coli 20 minute


title: Ecoli_untreated_20min_rep3


title: Ecoli_untreated_10min_rep3

source_name: Untreated E. coli 10 minute


title: Ecoli_untreated_10min_rep1


title: Ecoli_untreated_5min_rep1


title: Ecoli_untreated_10min_rep2


title: Ecoli_untreated_-5min_rep3

source_name: Untreated E. coli -5 minute


title: Ecoli_untreated_-5min_rep2


title: Ecoli_untreated_60min_rep2

source_name: Untreated E. coli 60 minute


title: Ecoli_untreated_20min_rep2


title: Ecoli_untreated_60min_rep3


title: Ecoli_untreated_60min_rep1


title: Naive_BGM1_Basal

status: Public on Jun 30 2008

city: Buenos Aires

first: Patricio

last: Yankilevich

address: Constitución 4234

country: Argentina

institute: BioSidus

description: The system first converts mRNA population in ds cDNA, followed by in vitro transcription and biotin labelling. Detection with Cy5-streptavidin.

hyb_protocol: After fragmentation, 8 µg of cRNA and CodeLink™ Human Whole Genome Bioarray were hybridized overnight at 37°C. The pre-arrayed 30-mer oligonucleotide slides contained over 45,000 well characterized human gene and transcripts.

scan_protocol: Slide was scanned at 635 nm for 3.5 s with 4.5 µm pixel size resolution in the arrayWoRx™ “e” scanner (Applied Precision, LLC, Issaquah, WA, USA.).

data_processing: Image analysis and raw data were assessed with CodeLink™ Expression Analysis software v4.1. Values obtained were globally normalized to the median expression value of the whole array spots.

source_name: RNA total basal

label_protocol:
CodeLink™ Expression Bioarray System (GE Healthcare Biosciences Corp, Sunnyvale, CA, USA) was used for sample preparation and hybridization.
Total RNA (0.5 μg) was primed for reverse transcription with oligo-d(T)24 containing the T7 RNA polymerase promoter site. After second-strand cDNA synthesis, the dscDNA served as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. IVT was performed by the linear amplification method in the presence of biotin-11-UTP to label the target cRNA (Perkin Elmer, Boston, MA, USA). Labeling with Cy5-streptavidin was performed.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using a Ficoll-Hypaque density gradient. After 24 hours of culture, non-adherent cells (mostly lymphocytes) were recovered, centrifuged, lysed and homogenized. Total RNA was isolated with the RNAeasy® Mini Kit extraction and purification system (QIAGEN Inc., Valencia, CA, USA) and analyzed for quality, integrity and DNA contamination by spectrophotometry and agarose gel electrophoresis prior to cDNA synthesis.

tag: Without treatment


title: Naive_PM4_Rebif

source_name: RNA total rebif

tag: 24 hr. cultivation with Rebif


title: Naive_PM1_Basal


title: Responder_PA4_Rebif

source_name: RNA total Rebif


title: Responder_PA3_Blastoferon

source_name: RNA total blastoferon

tag: 24 hr. cultivation with Blastoferon


title: Naive_BGM2_Control

source_name: RNA total control

tag: 24 hr. cultivation without product.


title: Responder_PA1_Basal


title: Naive_PM3_Blastoferon


title: Naive_BGM3_Blastoferon


title: Ecoli_untreated_-5min_rep1


title: Naive_BGM4_Rebif


title: Responder_AM2_Control


title: Responder_AM3_Blastoferon


title: NonResponder_MME4_Rebif


title: 1xMIC thiazin for 30min, biological rep3

status: Public on Jun 01 2008

city: Schwabenheim

first: Elena

last: Melnikow

address: Zur Propstei

department: Drug Discovery

country: Germany

institute: Intervet Innovation GmbH

description: Gene expression data from Pasteurella multocida treated with 1xmic thiazin for 30 min

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 16 hr at 45°C on a custom-made GeneChip Genome Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Pasteurella multocida

source_name: P. multocida treated with 1xmic thiazin for 30 min

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: P. multocida was cultured in 40 ml BHI medium for 3h at 37°C by 200 rpm.

extract_protocol: Extraction of total RNA was performed usind RNAeasy Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 1xMIC of each antibiotic was added to the P. multocida culture for 10 min and 30 min at an optical density of approximately 0.5. The bacteria were harvested by centifugation for 5 min at 5000 rpm at 4 °C.

tag: Strain

tag: Treatment

value: 1xmic thiazin for 30 min


title: 1xMIC thiazin for 30min, biological rep1


title: 1xMIC thiazin for 30min, biological rep2


title: Responder_AM4_Rebif


title: Responder_AM1_Basal


title: 1xMIC thiazin for 10min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic thiazin for 10 min

source_name: P. multocida treated with 1xmic thiazin for 10 min

value: 1xmic thiazin for 10 min


title: NonResponder_MME1_Basal


title: NonResponder_MME3_Blastoferon


title: Ecoli_untreated_5min_rep3


title: Naive_PM2_Control

tag: 24 hr. cultivation without product


title: NonResponder_MME2_Control


title: 1xMIC thiazin for 10min, biological rep1


title: 1xMIC thiazin for 10min, biological rep2


title: 1xMIC rifampin for 30min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic rifampin for 30 min

source_name: P. multocida treated with 1xmic rifampin for 30 min

value: 1xmic rifampin for 30 min


title: 1xMIC rifampin for 30min, biological rep1


title: control, biological rep16

description: Gene expression data from untreated Pasteurella multocida

source_name: P. multocida at OD(578) 0.5+-0.1 (control)

value: untreated cells. control for thiazin samples.


title: Ecoli_treated_cefsulodin60_10min_rep2

source_name: Treated E. coli 60 ug/ml cefsulodin 10 minute


title: control, biological rep17


title: 1xMIC rifampin for 10min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic rifampin for 10 min

source_name: P. multocida treated with 1xmic rifampin for 10 min

value: 1xmic rifampin for 10 min


title: 1xMIC rifampin for 10min, biological rep2


title: 1xMIC rifampin for 30min, biological rep2


title: control, biological rep18


title: 1xMIC cefquinome for 30min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic cefquinome for 30 min

source_name: P. multocida treated with 1xmic cefquinome for 30 min

value: 1xmic cefquinome for 30 min


title: 1xMIC cefquinome for 30min, biological rep2


title: Responder_PA2_Control

source_name: total RNA control


title: 1xMIC cefquinome for 30min, biological rep1


title: 1xMIC cefquinome for 10min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic cefquinome for 10 min

source_name: P. multocida treated with 1xmic cefquinome for 10 min

value: 1xmic cefquinome for 10 min


title: 1xMIC cefquinome for 10min, biological rep1


title: control, biological rep15

value: untreated cells. control for cefquinome and rifampin samples.


title: control, biological rep14


title: control, biological rep13


title: 1xMIC brodimoprim for 30min, biological rep1

description: Gene expression data from Pasteurella multocida treated with 1xmic brodimoprim for 30 min

source_name: P. multocida treated with 1xmic brodimoprim for 30 min

value: 1xmic brodimoprim for 30 min


title: 1xMIC brodimoprim for 30min, biological rep2


title: 1xMIC trimethoprim for 10min, biological rep1

description: Gene expression data from Pasteurella multocida treated with 1xmic trimethoprim for 10 min

source_name: P. multocida treated with 1xmic trimethoprim for 10 min

value: 1xmic trimethoprim for 10 min


title: 1xMIC trimethoprim for 30min, biological rep1

description: Gene expression data from Pasteurella multocida treated with 1xmic trimethoprim for 30 min

source_name: P. multocida treated with 1xmic trimethoprim for 30 min

value: 1xmic trimethoprim for 30 min


title: 1xMIC trimethoprim for 30min, biological rep3


title: 1xMIC trimethoprim for 30min, biological rep2


title: 1xMIC trimethoprim for 10min, biological rep3


title: 1xMIC brodimoprim for 30min, biological rep3


title: 1xMIC trimethoprim for 10min, biological rep2


title: 1xMIC brodimoprim for 10min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic brodimoprim for 10 min

source_name: P. multocida treated with 1xmic brodimoprim for 10 min

value: 1xmic brodimoprim for 10 min


title: 1xMIC brodimoprim for 10min, biological rep2


title: 1xMIC brodimoprim for 10min, biological rep1


title: 1xMIC cefquinome for 10min, biological rep2


title: 1xMIC tilmicosin for 30min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic tilmicosin for 30 min

source_name: P. multocida treated with 1xmic tilmicosin for 30 min

value: 1xmic tilmicosin for 30 min


title: 1xMIC tilmicosin for 10min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic tilmicosin for 10 min

source_name: P. multocida treated with 1xmic tilmicosin for 10 min

value: 1xmic tilmicosin for 10 min


title: 1xMIC tilmicosin for 30min, biological rep1


title: 1xMIC tilmicosin for 30min, biological rep2


title: control, biological rep11

value: untreated cells. control for tilmicosin, brodimoprim and trimethoprim samples.


title: 1xMIC tilmicosin for 10min, biological rep1


title: control, biological rep12


title: 1xMIC tilmicosin for 10min, biological rep2


title: 1xMIC florfenicol for 30min, biological rep2

description: Gene expression data from Pasteurella multocida treated with 1xmic florfenicol for 30 min

source_name: P. multocida treated with 1xmic florfenicol for 30 min

value: 1xmic florfenicol for 30 min


title: 1xMIC florfenicol for 30min, biological rep1


title: 1xMIC florfenicol for 10min, biological rep2

description: Gene expression data from Pasteurella multocida treated with 1xmic florfenicol for 10 min

source_name: P. multocida treated with 1xmic florfenicol for 10 min

value: 1xmic florfenicol for 10 min


title: 1xMIC florfenicol for 10min, biological rep1


title: 1xMIC florfenicol for 10min, biological rep3


title: control, biological rep9

value: untreated cells. control for florfenicol samples.


title: 1xMIC florfenicol for 30min, biological rep3


title: control, biological rep6

value: untreated cells. control for enrofloxacin samples.


title: 1xMIC enrofloxacin for 10min, biological rep1

description: Gene expression data from Pasteurella multocida treated with 1xmic enrofloxacin for 10 min

source_name: P. multocida treated with 1xmic enrofloxacin for 10 min

value: 1xmic enrofloxacin for 10 min


title: control, biological rep10


title: control, biological rep4


title: 1xMIC enrofloxacin for 10min, biological rep3


title: 1xMIC enrofloxacin for 10min, biological rep2


title: 1xMIC enrofloxacin for 30min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xmic enrofloxacin for 30 min

source_name: P. multocida treated with 1xmic enrofloxacin for 30 min

value: 1xmic enrofloxacin for 30 min


title: 1xMIC enrofloxacin for 30min, biological rep2


title: 1xMIC rifampin for 10min, biological rep1

value: 1xmic rifampin for 10 min


title: 1xMIC enrofloxacin for 30min, biological rep1


title: control, biological rep7


title: 1xMIC novobiocin for 30min, biological rep2

description: Gene expression data from Pasteurella multocida treated with 1xMIC novobiocin for 30min

source_name: P. multocida treated with 1xmic novobiocin for 30 min

value: 1xmic novobiocin for 30 min


title: 1xMIC novobiocin for 30min, biological rep1


title: 1xMIC novobiocin for 10min, biological rep3

description: Gene expression data from Pasteurella multocida treated with 1xMIC novobiocin for 10min

source_name: P. multocida treated with 1xmic novobiocin for 10 min

value: 1xmic novobiocin for 10 min


title: 1xMIC novobiocin for 10min, biological rep1


title: 1xMIC novobiocin for 10min, biological rep2


title: control, biological rep3

source_name: P. multocida at OD(578) 0.5+-0.1 (control)

value: untreated cells. control for novobiocin samples.


title: control, biological rep2


title: control, biological rep5


title: control, biological rep8


title: MLS009B

city: Columbus

first: Ping

last: Pei

state: OH

address: 305 West 12th Ave

department: Oral Pathology

institute: OSU

description: Gene expression data from pretreated oral tissue

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the human genoma gene chip U133A 2.0 Plus. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

source_name: human oral tissue

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Tissue was immediately placed in RNA later and stored at -80 degrees until RNA processing by routine methods.

extract_protocol: Total RNA extration was performed by using Absolutely RNA Miniprep Kit according to the manufacturer's instructions.

treatment_protocol: Patients applied a 10% freeze dried black raspberry gel to treatment site four times daily for six weeks.  Pretreatment-baseline-no gel yet applied.

tag: pretreated oral tissue


title: control, biological rep1

description: Gene expression data from untreated Pasteurella multocida


title: MLS012B


title: MLS010B


title: MLS006B


title: MLS013A

description: Gene expression data from post treated oral tissue

tag: post treated oral tissue


title: MLS008A


title: MLS010A


title: MLS007B


title: MLS011A


title: MLS011B


title: MLS007A


title: MLS014A


title: MLS012A


title: MLS008B


title: MLS009A


title: MLS014B


title: MLS002B


title: MLS003A


title: MLS006A


title: MLS005A


title: MLS002A


title: MLS003B


title: MLS005B


title: MLS001B


title: MLS001A


title: YRV_N48

status: Public on Apr 30 2008

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

description: Y-chromosome substitution line

hyb_protocol: Genisphere 3DNA system

scan_protocol: Axon Scanner and Genepix

data_processing: The ratios were taken from the Limma package after loess normalization of the raw intensities data originally obtained in Genepix.

organism: Drosophila melanogaster

label_protocol: Genisphere 3DNA system

extract_protocol: Standard total RNA preps wih Trizol

tag: Line

value: Yz53; Sex:Female

source_name: Ycs

extract_protocol: Standard total RNA preps with Trizol

value: Ycs; Sex:Female


title: YRV_N59

description: Y-chromosome substitution line


title: YRV_F68

description: Y-chromosome substitution line


title: YRV_F39

description: Y-chromosome substitution line


title: MLS013B


title: YRV_N9

description: Y-chromosome substitution line

source_name: Ycongo

value: Ycongo; Sex:male; Temperature:25'C

source_name: Ymass

value: Ymass; Sex:male; Temperature:25'C


title: YRV_N42

description: Y-chromosome substitution line

value: Yz53; Sex:male

value: Ycs; Sex:male


title: YRV_N46

description: Y-chromosome substitution line

value: Ymass; Sex:male; Temperature:16'C


title: YRV_N74

description: Y-chromosome substitution line


title: YRV_F32

description: Y-chromosome substitution line


title: YRV_N80

description: Y-chromosome substitution line

value: Ycongo; Sex:male; Temperature:16'C


title: YRV_N79

description: Y-chromosome substitution line


title: YRV_N47

description: Y-chromosome substitution line


title: YRV_N41

description: Y-chromosome substitution line


title: YRV_N60

description: Y-chromosome substitution line


title: YRV_N63

description: Y-chromosome substitution line


title: YRV_F37

description: Y-chromosome substitution line


title: YRV_N8temp

description: Y-chromosome substitution line

value: Ycongo16; Sex:male; Temperature:16'C

value: Ymass16; Sex:male; Temperature:16'C


title: YRV_N44

description: Y-chromosome substitution line


title: YRV_F34

description: Y-chromosome substitution line


title: YRV_F36

description: Y-chromosome substitution line


title: YRV_F33

description: Y-chromosome substitution line


title: YRV_F38

description: Y-chromosome substitution line


title: YRV_N39

description: Y-chromosome substitution line


title: YRV_N45

description: Y-chromosome substitution line


title: YRV_F35

description: Y-chromosome substitution line


title: YRV_N65

description: Y-chromosome substitution line


title: YRV_N40

description: Y-chromosome substitution line

value: Ycongo; Sex:male

value: Y4361; Sex:male


title: YRV_N13

description: Y-chromosome substitution line


title: YRV_N37

description: Y-chromosome substitution line

value: Ymass; Sex:male


title: YRV_N35

description: Y-chromosome substitution line


title: YRV_N16

description: Y-chromosome substitution line


title: YRV_N34

description: Y-chromosome substitution line


title: YRV_N17

description: Y-chromosome substitution line


title: YRV_N36

description: Y-chromosome substitution line


title: IPEC_CholeraToxin_8h_rep3

status: Public on Apr 01 2008

city: St. Paul

first: Cheryl

last: Dvorak

state: MN

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

description: Experiment was performed in triplicate for a total of 6 Affymetrix chips.

hyb_protocol: Hybridized to the Affymetrix porcine genome chip at the University of Minnesota Biomedical Genomics Center following manufacturers protocols

scan_protocol: Scanned at the University of Minnesota Biomedical Genomics Center following manufacturers protocols

data_processing: The 6 .CEL files were then analyzed together using the RMA algorithm in the Genedata Expressionist software at the University of Minnesota Supercomputing Institute. Ratio of means/fold changes were determined using the average intensity of 3 CT treated samples over the average intensity of the 3 un-treated samples

organism: Sus scrofa

source_name: IPEC-J2 cells grown in transwells, 8h treatment

label_protocol: 5 ug total RNA was labeled using the GeneChip® One-Cycle Target Labeling and Control Reagents according to manufacturers protocols

growth_protocol: Cells were seeded at 5 X 105 cells/ml in 6-well transwell dishes (Corning, inc., Lowell, MA) for experiments and incubated in 5% CO2 for 7-10 days before treatment, with media changed every 3-4 days. TEER measurements were taken every 3 days, before changing media. Confluent monolayers were used at day 7-10, 24 hours after TEER measurements were over 1000 Ω (>2000 Ω cm2).

extract_protocol: After desired time points the top and bottom buffers were removed, cell monolayers were washed 3 times with PBS, and incubated with trypsin for 15-20 minutes at 37°C in 5% CO2. Cells were harvested and either frozen at -80, or immediately used for total RNA isolation using the Qiagen RNeasy mini kit protocol.

treatment_protocol: Grown 8h in media with 50 ng/ml cholera toxin added to transwells containing a confluent monolayer of IPEC-J2 in a volume of 15 ul or less

tag: Intestinal porcine epithelial cell line IPEC-J2

tag: Grown on transwell plates for 7-10 days until confluent monolayers with TEER>1000 ohms

tag: Treated with CT for 8h


title: YRV_N12

description: Y-chromosome substitution line


title: YRV_D98

description: Y-chromosome substitution line


title: YRV_N8

description: Y-chromosome substitution line


title: YRV_D88

description: Y-chromosome substitution line


title: YRV_D86

description: Y-chromosome substitution line


title: YRV_D87

description: Y-chromosome substitution line


title: YRV_N10

description: Y-chromosome substitution line


title: YRV_D65

description: Y-chromosome substitution line

scan_protocol: Axon scanner and Genepix

extract_protocol: Standard trizol total RNA


title: YRV_D68

description: Y-chromosome substitution line


title: YRV_D85

description: Y-chromosome substitution line

value: Ycs; Sex:Male

value: Y4361; Sex:Male


title: YRV_D36

description: Y-chromosome substitution line

value: Ycongo; Sex:male; Age:3 days old adults

value: Ymass; Sex:male; Age:3 days old adults


title: YRV_E47

description: Y-chromosome substitution line


title: YRV_D75

description: Y-chromosome substitution line


title: YRV_N19

description: Y-chromosome substitution line


title: IPEC_CholeraToxin_8h_rep2


title: RIMD2212924 replicate3

status: Public on Mar 31 2008

type: genomic

city: Suita

first: Kaori

last: Izutsu

state: Osaka

address: 1-1 Yamadaoka

department: Research Institute for Microbial Diseases

country: Japan

institute: Osaka University

description: RIMD2212924 replicate3

hyb_protocol: Cy3- or Cy5- labeled probes (18 µl for each) were mixed, and 3 µl of 10% SDS, 6 µl of 25 mg/ml yeast tRNA and 15 µl of 20X SSC (3 M NaCl, 0.3 M trisodium citrate 2H2O, pH 7.0) were added to the mixture. After incubation at 96ºC for 2 min, the denatured sample was applied to a microarray slide and incubated on an MAUI hybridization chamber at 60ºC for 16 h. The slide was then washed twice in 2X SSC/0.1% SDS solution at 60°C for 10 min, twice in 0.2X SSC/0.1% SDS solution at room temperature for 10 min, and twice in 0.2X SSC solution at room temperature for another 10 min. Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.

scan_protocol: Scanned with a ScanArrayExpress scanner (PerkinElmer). Obtained data were analyzed by the ScanArrayExpress software ver.3.0.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Cy3 signal/processed Cy5 signal.

molecule: genomic DNA

organism: Vibrio parahaemolyticus

label_protocol: First, 2 µg of genomic DNA was labeled with aminoallyl-modified dUTP (Sigma) using the Bioprime DNA Labeling System (Invitrogen). DNAs were not sheared or digested by restriction enzymes prior to the labeling. The aminoallyl-labeled DNA was purified by phenol-chloroform extraction and ethanol precipitation. , Precipitated DNA was dried and resuspended in 10 µl of 50 mM NaHCO3. After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (Amersham), the sample was incubated at room temperature in the dark for 1 h to allow the dye to couple with DNA. The fluorescently labeled DNA was finally purified by the CentriCep spin column (Princeton Sepatations Inc.).

growth_protocol: Cells were grown to the stationary phase at 37ºC in Luria-Bertani containing medium3% NaCl .

extract_protocol: Genomic DNA was purified using the DNeasy Tissue Kit (Qiagen) according to the manufacturer's instruction.

tag: sequenced strain

tag: KP+, pandemic strain


title: RIMD2212924 replicate2

description: RIMD2212924 replicate2


title: RIMD2212924 replicate1

description: RIMD2212924 replicate1


title: RIMD2210633 replicate1

description: RIMD2210633 replicate1


title: RIMD2212686 replicate2

description: RIMD2212686 replicate2


title: RIMD2212686 replicate1

description: RIMD2212686 replicate1


title: RIMD2210633 replicate2

description: RIMD2210633 replicate2


title: RIMD2210633 replicate3

description: RIMD2210633 replicate3


title: RIMD2212686 replicate3

description: RIMD2212686 replicate3


title: IPEC_NoTreatment_8h_rep1

treatment_protocol: Grown 8h in media without treatments added.

tag: Untreated for 8h (compared with CT treated for 8h)


title: YRV_N11

description: Y-chromosome substitution line

value: Ymass; Sex:male; Temperature 25'C


title: IPEC_CholeraToxin_8h_rep1


title: RIMD2210600 replicate3

description: RIMD2210600 replicate3

tag: KP+, non-pandemic strain


title: IPEC_NoTreatment_8h_rep3

treatment_protocol: Grown 8h in media without treatments added

tag: Untreated for 8h


title: RIMD2210600 replicate2

description: RIMD2210600 replicate2


title: RIMD2210612 replicate2

description: RIMD2210612 replicate2


title: RIMD2210612 replicate3

description: RIMD2210612 replicate3


title: RIMD2210587 replicate1

description: RIMD2210587 replicate1


title: RIMD2210600 replicate1

description: RIMD2210600 replicate1


title: RIMD2210587 replicate3

description: RIMD2210587 replicate3


title: RIMD2210612 replicate1

description: RIMD2210612 replicate1


title: RIMD2210587 replicate2

description: RIMD2210587 replicate2


title: RIMD22121044 replicate3

description: RIMD22121044 replicate3


title: RIMD2210706 replicate3

description: RIMD2210706 replicate3


title: RIMD2210706 replicate1

description: RIMD2210706 replicate1


title: RIMD2210706 replicate2

description: RIMD2210706 replicate2


title: RIMD22121044 replicate2

description: RIMD22121044 replicate2


title: RIMD22121044 replicate1

description: RIMD22121044 replicate1


title: RIMD2211932 replicate3

description: RIMD2211932 replicate3


title: MaPTOL on MmREST

type: MPSS

city: San Diego

first: Olivier

last: Harismendy

state: CA

address: 10550 North Torrey PInes Road

department: Neurobiology

institute: The Scripps Research Institute

description: not applicable

data_processing:
The short sequence reads were processed automatically and sequences flanked by two CATG motifs were extracted. MaPTags with a length between 30 to 36 nucleotides (variation that is inherent in MmeI digestion) were retained for the analysis. MaPTags were then consolidated with their reverse complement and grouped by unique sequences.
The first 14 nucleotides of each MaPTag indexed after the CATG were used to search the Mouse Genome database (UCSC mm8). Only perfect matches were accepted. If a hit was found, then a match to the last 14 nucleotides was sought by searching up to 3kb downstream of the first hit, on the same strand in the opposite orientation. If both halves of a MaPTag were found, the junction between the 2 halves of the tag was then compared to the genome sequence. If the junction region also matched (with up to 1 mismatch allowed), then the tag was considered a hit and the location was defined as a MaPTag locus. MaPTags with slightly different sequences but the same location (due to variation in the position of Mme1 digestion within the same cloned fragment), were consolidated into one locus. All of the loci are associated with their count number, number of intervening CATG in the locus, and the percentage of each half tag located in a repeated region.

organism: Mus musculus

source_name: E12.5 embryos

extract_protocol: Chromatin was prepared from mouse E12.5 embryos, sheared by sonication, and precleared with Protein-G agarose beads according to {Weinmann, 2002 #6}. An antibody (REST-H290 – Santa Cruz) targeted against the N-terminal region of mouse REST was used for immunoprecipitation under standard ChIP conditions {Weinmann, 2002 #6} with the following modifications. Two rounds of immunoprecipitation were carried on successively. During the second ChIP, after washing the bead-chromatin complex, they were equilibrated in NEB restriction enzyme buffer 4 with 0.5 % NP40 to sequester SDS. 80 µl of beads-chromatin slurry were then digested for 6hrs with 80 units of NlaIII. This step facilitates cloning of the co-immunoprecipitated DNA fragment and also provides footprint information as proteins that are bound to the DNA may prevent cleavage. After digestion, the complexes were again washed, eluted, and crosslinks reversed according to standard protocols {Weinmann, 2002 #6}. The entire eluate was cloned into the tagging vector pTagBM that contains two head to head MmeI restriction sites flanking the SphI cloning site. This initial library was amplified in bacteria (ECLONI – Lucigen) and purified using Invitrogen MaxiPrep Filter kit. 5 µg of this library was digested by 192 U of MmeI restriction enzyme overnight. After inactivation of the enzyme, we blunted the cut plasmid by incubation with 6U of T4 DNA polymerase and 10 pmol of dNTP during 3hrs at 14ºC. We stopped the reaction by addition of 10 mM EDTA for 20 min at 75ºC. The cut library was then purified by separation on an agarose gel and gel extraction using Qiagen Gel Extraction kit. 50 ng of the library was religated by overnight incubation at 14ºC with 1 µl of Invitrogen T4 DNA ligase. The religated library was used to transform E. coli competent cells (ECLONI – Lucigen). After quality control for religation by PCR, the library was amplified by growth on LB agar dishes (25x25 cm) and purified using Invitrogen MaxiPrep Filter kit. 100 µg of the library was digested overnight by 500 U of BamH1 restriction enzyme which sites encompass the two Mme1 sites on the pTagBM vector. The MaPTags extracted during this process were purified on an 8% polyacrylamide-TBE gel and electro-eluted from the gel (BioRad). 10 µg of MaPTags were subjected to sequencing.

tag: E12.5 embryos


title: RIMD2210884 replicate3

description: RIMD2210884 replicate3


title: RIMD2210086 replicate1

description: RIMD2210086 replicate1


title: RIMD2210086 replicate2

description: RIMD2210086 replicate2


title: RIMD2211499 replicate1

description: RIMD2211499 replicate1


title: RIMD2211932 replicate1

description: RIMD2211932 replicate1


title: RIMD2211932 replicate2

description: RIMD2211932 replicate2


title: RIMD2211499 replicate2

description: RIMD2211499 replicate2


title: RIMD2211499 replicate3

description: RIMD2211499 replicate3


title: RIMD2210086 replicate3

description: RIMD2210086 replicate3


title: RIMD2210884 replicate2

description: RIMD2210884 replicate2


title: RIMD2210056 replicate3

description: RIMD2210056 replicate3


title: RIMD2210056 replicate1

description: RIMD2210056 replicate1


title: RIMD2210884 replicate1

description: RIMD2210884 replicate1


title: RIMD2210056 replicate2

description: RIMD2210056 replicate2


title: SNL+ GPN sc, contra set C

city: North Brunswick

first: Jason

middle: Gang

last: Jin

address: 675 US Highway

institute: MaxyBio

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug 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.

organism: Rattus norvegicus

source_name: Rat hemisected spinal cord, contralateral (contra) to the injury.

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

growth_protocol: For gene expression analysis, rats from five experimental groups were sacrificed 19–21 days after surgery

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Rats having the L5-L6 spinal nerves ligated (SNL) were performed, Sham-operation consisted of exposing the spinal nerves without ligation or manipulation. Naïve animals did not receive surgery.Rats were tested before and 12–14 days after surgery. Only SNL rats exhibiting a significantly reduced PWT in the ipsilateral limb were included in drug testing or gene expression studies (eight to twelve rats per group). Vehicle (0.9% saline) or gabapentin (GPN; 100 mg/kg dissolved in 0.9% saline) was administered intraperitoneally (i.p.) once a day for 7 days in a volume of 2 ml/kg. On the last (7th) treatment day (corresponding to 19–21 days post-surgery), rats were again assessed by PWT, in particular to confirm the reversal of neuropathic pain with GPN treatment.


title: SNL+ GPN L6 DRG,Contra set C

description: Gene expression data

source_name: Rat L6 dorsal root ganglia (DRG), contralateral (contra) to the injury.

tag: rats from five experimental groups were sacrificed 19–21 days after surgery


title: SNL+ GPN nerve,contra set C

description: Gene expression data

source_name: Rat mid thigh sciatic nerve, contralateral (contra) to the injury.


title: SNL+ GPN brain set C

description: Gene expression data

source_name: Rat whole brain


title: RIMD2210883 replicate3

description: RIMD2210883 replicate3


title: SNL+ GPN sc,Ipsi set C

description: Gene expression data

source_name: Rat hemisected spinal cord, ipsilateral(ipsi) to the injury.


title: RIMD2210554 replicate3

description: RIMD2210554 replicate3

tag: KP-, non-pandemic strain


title: SNL+ GPN L4 DRG,Contra set C

description: Gene expression data

source_name: Rat L4 dorsal root ganglia (DRG), contralateral (contra) to the injury.


title: SNL+ GPN nerve,Ipsi set C

description: Gene expression data

source_name: Rat mid thigh sciatic nerve, ipsilateral(ipsi) to the injury.


title: RIMD2210554 replicate1

description: RIMD2210554 replicate1


title: RIMD2210554 replicate2

description: RIMD2210554 replicate2


title: SNL+ GPN L5 DRG,Contra set C

description: Gene expression data

source_name: Rat L5 dorsal root ganglia (DRG), contralateral (contra) to the injury.


title: SNL L4 DRG,Contra set C

description: Gene expression data


title: SNL L5 DRG,Contra set C

description: Gene expression data


title: SNL+ GPN L4 DRG,Ipsi set C

description: Gene expression data

source_name: Rat L4 dorsal root ganglia (DRG), ipsilateral(ipsi) to the injury.


title: RIMD2210883 replicate2

description: RIMD2210883 replicate2


title: SNL+ GPN L6 DRG,Ipsi set C

description: Gene expression data

source_name: Rat L6 dorsal root ganglia (DRG), ipsilateral(ipsi) to the injury.


title: SNL+ GPN L5 DRG,Ipsi set C

description: Gene expression data

source_name: Rat L5 dorsal root ganglia (DRG), ipsilateral(ipsi) to the injury.


title: SNL brain set C

description: Gene expression data


title: SNL L6 DRG,Contra set C

description: Gene expression data


title: RIMD2210883 replicate1

description: RIMD2210883 replicate1


title: RIMD2210536 replicate3

description: RIMD2210536 replicate3


title: SNL sc, contra set C

description: Gene expression data


title: SNL nerve,Ipsi set C

description: Gene expression data


title: RIMD2210536 replicate2

description: RIMD2210536 replicate2


title: IPEC_NoTreatment_8h_rep2


title: YRV_N38

description: Y-chromosome substitution line


title: RIMD2210536 replicate1

description: RIMD2210536 replicate1


title: RIMD2210856 replicate3

description: RIMD2210856 replicate3


title: RIMD2210856 replicate2

description: RIMD2210856 replicate2


title: RIMD2210911 replicate3

description: RIMD2210911 replicate3


title: Sham L4 DRG,Contra set C

description: Gene expression data


title: Sham L6 DRG,Contra set C

description: Gene expression data


title: SNL L5 DRG,Ipsi set C

description: Gene expression data


title: SNL L4 DRG, Ipsi set C

description: Gene expression data


title: Sham brain set C

description: Gene expression data


title: RIMD2210911 replicate2

description: RIMD2210911 replicate2


title: Sham nerve,contra set C

description: Gene expression data


title: Sham L5 DRG,Contra set C

description: Gene expression data


title: Sham sc,Ipsi set C

description: Gene expression data


title: SNL L6 DRG,Ipsi set C

description: Gene expression data


title: Sham sc, contra set C

description: Gene expression data


title: RIMD2210911 replicate1

description: RIMD2210911 replicate1


title: Sham nerve,Ipsi set C

description: Gene expression data


title: Sham L6 DRG,Ipsi set C

description: Gene expression data


title: RIMD2210001 replicate3

description: RIMD2210001 replicate3


title: SNL sc,Ipsi set C

description: Gene expression data


title: Naive+ GPN L6 DRG,Contra set C

description: Gene expression data


title: Sham L5 DRG,Ipsi set C

description: Gene expression data


title: RIMD2210856 replicate1

description: RIMD2210856 replicate1


title: RIMD2210470 replicate2

description: RIMD2210470 replicate2

tag: non-pathogenic strain


title: Naive+ GPN brain set C

description: Gene expression data


title: RIMD2210001 replicate1

description: RIMD2210001 replicate1


title: RIMD2210470 replicate3

description: RIMD2210470 replicate3


title: RIMD2210001 replicate2

description: RIMD2210001 replicate2


title: Naive+ GPN nerve,Ipsi set C

description: Gene expression data


title: Sham L4 DRG, Ipsi set C

description: Gene expression data


title: Naive+ GPN sc,Ipsi set C

description: Gene expression data


title: Naive+ GPN L5 DRG,Ipsi set C

description: Gene expression data


title: Naive+ GPN L6 DRG,Ipsi set C

description: Gene expression data


title: Naive+ GPN sc, contra set C

description: Gene expression data


title: SNL+ GPN sc, contra set B

description: Gene expression data


title: SNL+ GPN brain set B

description: Gene expression data


title: RIMD2210470 replicate1

description: RIMD2210470 replicate1


title: Naive+ GPN L4 DRG,Contra set C

description: Gene expression data


title: SNL+ GPN nerve,contra set B

description: Gene expression data


title: SNL+ GPN L6 DRG,Contra set B

description: Gene expression data


title: Naive+ GPN L4 DRG,Ipsi set C

description: Gene expression data


title: SNL+ GPN L5 DRG,Contra set B

description: Gene expression data


title: Naive brain set C

description: Gene expression data


title: Naive+ GPN nerve,contra set C

description: Gene expression data


title: Naive sc, contra set C

description: Gene expression data


title: RIMD2210384 replicate2

description: RIMD2210384 replicate2


title: Naive nerve,contra set C

description: Gene expression data


title: Naive L5 DRG,Contra set C

description: Gene expression data


title: RIMD2210384 replicate3

description: RIMD2210384 replicate3


title: RIMD2210384 replicate1

description: RIMD2210384 replicate1


title: SNL+ GPN sc,Ipsi set B

description: Gene expression data


title: SNL+ GPN nerve,Ipsi set B

description: Gene expression data


title: Naive L4 DRG,Contra set C

description: Gene expression data


title: SNL+ GPN L4 DRG,Contra set B

description: Gene expression data


title: Naive sc,Ipsi set C

description: Gene expression data


title: SNL+ GPN L6 DRG,Ipsi set B

description: Gene expression data


title: Naive L6 DRG,Ipsi set C

description: Gene expression data


title: Naive nerve,Ipsi set C

description: Gene expression data


title: RIMD2212201 replicate3

description: RIMD2212201 replicate3


title: SNL+ GPN L5 DRG,Ipsi set B

description: Gene expression data


title: RIMD2212201 replicate2

description: RIMD2212201 replicate2


title: SNL+ GPN sc, contra set A

description: Gene expression data


title: Naive L4 DRG,Ipsi set C

description: Gene expression data


title: SNL+ GPN L4 DRG,Ipsi set B

description: Gene expression data


title: SNL+ GPN L5 DRG,Contra set A

description: Gene expression data


title: RIMD2212201 replicate1

description: RIMD2212201 replicate1


title: SNL+ GPN brain set A

description: Gene expression data


title: SNL L5 DRG,Contra set B

description: Gene expression data


title: SNL+ GPN L4 DRG,Contra set A

description: Gene expression data


title: SNL+ GPN sc,Ipsi set A

description: Gene expression data


title: SNL+ GPN L6 DRG,Ipsi set A

description: Gene expression data


title: Naive L5 DRG,Ipsi set C

description: Gene expression data


title: SNL+ GPN L6 DRG,Contra set A

description: Gene expression data


title: SNL+ GPN L5 DRG,Ipsi set A

description: Gene expression data


title: SNL sc, contra set B

description: Gene expression data


title: SNL+ GPN L4 DRG,Ipsi set A

description: Gene expression data


title: SNL brain set B

description: Gene expression data


title: SNL+ GPN nerve,Ipsi set A

description: Gene expression data


title: SNL L4 DRG,Contra set A

description: Gene expression data


title: SNL L5 DRG,Contra set A

description: Gene expression data


title: SNL brain set A

description: Gene expression data


title: SNL L4 DRG,Contra set B

description: Gene expression data


title: SNL L6 DRG,Contra set B

description: Gene expression data


title: SNL L6 DRG,Contra set A

description: Gene expression data


title: SNL sc,Ipsi set B

description: Gene expression data


title: SNL L6 DRG,Ipsi set B

description: Gene expression data


title: SNL sc, contra set A

description: Gene expression data


title: SNL nerve,Ipsi set A

description: Gene expression data


title: SNL L5 DRG,Ipsi set B

description: Gene expression data


title: SNL nerve,Ipsi set B

description: Gene expression data


title: Sham brain set B

description: Gene expression data


title: Sham sc, contra set A

description: Gene expression data


title: Sham L6 DRG,Contra set B

description: Gene expression data


title: SNL L4 DRG, Ipsi set B

description: Gene expression data


title: Sham L5 DRG,Contra set A

description: Gene expression data


title: Sham sc, contra set B

description: Gene expression data


title: Sham L6 DRG,Contra set A

description: Gene expression data


title: SNL L6 DRG,Ipsi set A

description: Gene expression data


title: SNL L5 DRG,Ipsi set A

description: Gene expression data


title: Sham nerve,contra set A

description: Gene expression data


title: Sham L5 DRG,Contra set B

description: Gene expression data


title: SNL sc,Ipsi set A

description: Gene expression data


title: Sham sc,Ipsi set A

description: Gene expression data


title: Sham nerve,Ipsi set B

description: Gene expression data


title: Sham L4 DRG,Contra set B

description: Gene expression data


title: Sham L4 DRG,Contra set A

description: Gene expression data


title: Sham sc,Ipsi set B

description: Gene expression data


title: Sham nerve,contra set B

description: Gene expression data


title: Sham brain set A

description: Gene expression data


title: SNL L4 DRG, Ipsi set A

description: Gene expression data


title: Sham nerve,Ipsi set A

description: Gene expression data


title: Sham L6 DRG,Ipsi set A

description: Gene expression data


title: SNL+ GPN nerve,contra set A

description: Gene expression data


title: Naive+ GPN brain set A

description: Gene expression data


title: Sham L6 DRG,Ipsi set B

description: Gene expression data


title: Sham L5 DRG,Ipsi set B

description: Gene expression data


title: Sham L4 DRG, Ipsi set A

description: Gene expression data


title: Sham L4 DRG, Ipsi set B

description: Gene expression data


title: Naive+ GPN nerve,contra set B

description: Gene expression data


title: Naive+ GPN sc, contra set A

description: Gene expression data


title: Naive+ GPN brain set B

description: Gene expression data


title: Naive+ GPN sc, contra set B

description: Gene expression data


title: Naive+ GPN nerve,Ipsi set A

description: Gene expression data


title: Naive+ GPN L6 DRG,Ipsi set A

description: Gene expression data


title: Naive+ GPN sc,Ipsi set A

description: Gene expression data


title: Naive+ GPN nerve,contra set A

description: Gene expression data


title: Naive+ GPN L6 DRG,Contra set B

description: Gene expression data


title: Sham L5 DRG,Ipsi set A

description: Gene expression data


title: Naive+ GPN L4 DRG,Contra set A

description: Gene expression data


title: Naive+ GPN L6 DRG,Ipsi set B

description: Gene expression data


title: Naive+ GPN nerve,Ipsi set B

description: Gene expression data


title: Naive+ GPN L5 DRG,Ipsi set A

description: Gene expression data


title: Naive+ GPN L4 DRG,Ipsi set A

description: Gene expression data


title: Naive+ GPN L4 DRG,Ipsi set B

description: Gene expression data


title: Naive brain set A

description: Gene expression data


title: Naive sc, contra set A

description: Gene expression data


title: Naive brain set B

description: Gene expression data


title: Naive+ GPN sc,Ipsi set B

description: Gene expression data


title: Naive L5 DRG,Contra set A

description: Gene expression data


title: Naive+ GPN L5 DRG,Ipsi set B

description: Gene expression data


title: Naive+ GPN L6 DRG,Contra set A

description: Gene expression data


title: Naive L5 DRG,Contra set B

description: Gene expression data


title: Naive nerve,contra set A

description: Gene expression data


title: Naive sc,Ipsi set B

description: Gene expression data


title: Naive L4 DRG,Contra set B

description: Gene expression data


title: Naive L4 DRG,Contra set A

description: Gene expression data


title: Naive sc,Ipsi set A

description: Gene expression data


title: Naive L6 DRG,Ipsi set B

description: Gene expression data


title: Naive nerve,Ipsi set A

description: Gene expression data


title: Naive L5 DRG,Ipsi set A

description: Gene expression data


title: Naive L4 DRG,Ipsi set B

description: Gene expression data


title: Naive L5 DRG,Ipsi set B

description: Gene expression data


title: Naive nerve,contra set B

description: Gene expression data


title: Naive L6 DRG,Ipsi set A

description: Gene expression data


title: Naive nerve,Ipsi set B

description: Gene expression data


title: Naive L4 DRG,Ipsi set A

description: Gene expression data


title: wild type array 3 subarray 1

status: Public on Mar 22 2008

type: mixed

city: Cleveland

first: Krisztina

middle: Margaret

last: Papp-Wallace

email: kmp12@case.edu, mem6@case.edu

address: 2109 Adelbert Road W317

department: Pharmacology

institute: Case Western Reserve Univeristy

description: CorA is the primary Mg2+ channel in Salmonella enterica serovar Typhimurium. Cells were collected for RNA isolation on three separate days from wild type or corA strains giving six total samples from three independent cultures for each strain. Genomic DNA from wild type was used as a reference on each slide.

hyb_protocol: Prepping slides for hybridization: 1. Warm up slide pre-hybridiztion solution (25% formamide, 5X SSC (Ambion #9763), 0.1% SDS, 0.1 mg/ml BSA) to 42°C in a Coplin jar (VWR# 25457-200) in a water bath. 2. Incubate microarray slides in pre-warmed hybridization solution for 60 min at 42°C. 3. Wash arrays 10X in glass Wheaton dishes (Wheaton Science Products #900200) with DI water. 4. Wash arrays 1X with isopropanol. 5. Dry arrays by centrifugation at 1000 rpm for 15-20 min. 6. Make hybridization buffer: 250 μl of formamide, 250 μl of 20X SSC, 490 μl of DI water, and add 10 μl 10% SDS last. Filter hybridization buffer with a 0.45 μm filter. 7. Heat probe at 95°C on heat block for 5-10 min and vortex to resuspend. 8. Warm up hybridization chambers (Corning #2551) with slides inside on heat block. 9. Add hot probe to center of hot slide. Hold cover slip at 45° angle close to slide surface and drop. Add hybridization buffer to the bottom of the chamber to keep it humidified. 10. Close up chambers, cover with foil, weigh down in 42°C water bath, and incubate overnight. Post-Hybridization and scanning: 1. Remove cover slips by holding slides upside down in warm (55°C) low stringency buffer (2X SSC and 0.1% SDS in dH20) in a large glass dish. Remove fallen cover slip and wash slides vigorously (move back and forth by hand quickly) in large glass dish for 2-3 min. The most important wash is the first wash, because that is when most of the excess dye comes off. Then wash 2 times for 5 min with warm (55°C) low stringency buffer (2X SSC and 0.1% SDS in dH20) in Wheaton dish on an orbital shaker or by hand on the benchtop mimicking an orbital shaker. Do not use DTT in wash buffers. Slightly old DTT will cause green film on slide, thus ruining the slide. Do not use ddH20 for wash buffers. Do not let slides dry out during washing process. Washing is very important to remove excess dye and decrease background. Extra washes will help remove excess dye and reduce background. 2. Wash slides vigorously 2 times for 5 min with room temperature medium stringency buffer (0.1X SSC and 0.1% SDS in dH20). 3. Wash slides vigorously 2 times for 5 min with room temperature high stringency buffer (0.1X SSC in dH20). 4. Wash slides in water 1 time for 3 min and transfer to centrifuge. 5. Dry slides by centrifugation for 15-20 min at 1000 rpm. 6. Slides should be kept in the dark until they are scanned.

scan_protocol: Slides were scanned using a GenePix 4000B microarray scanner. Slides should be scanned to obtain a ratio between 0.8-1.2 for Cy3/Cy5 fluorescence.

data_processing: The TM4 Microarray Suite produced by TIGR was used for data analysis (Saeed AI, 2003, Biotechniques). Spotfinder was used to assign gene identifiers to spots (circle algorithm) and to flag spots. MIDAS was used to normalize (Lowess (Locfit) and Standard Deviation Regularization) the data. The normalized data was imported into Microsoft Excel. Normalized intensity values for RNA were divided by those for the genomic DNA control for each slide to obtain a ratio. Three sets of ratios were obtained for wild type and three sets of ratios were obtained for a corA strain.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: wild type

label_protocol: Part 1: 1. Using RNase free tubes, mix: 30 μg of total RNA, 2 μl random hexamers (3 mg/ml) (Invitrogen #48190-011), 1 μl RNaseOUT (Invitrogen #10777-019), and bring to 18.5 μl with DEPC water. 2. For RNA labeling, mix well, incubate at 70°C for 10 min, snap freeze in a dry ice/ethanol bath for 30 sec, centrifuge briefly, and bring to room temperature. 3. Mix the following: 18.5 μl of RNA/primer mix from above step, 6 μl 5X first strand buffer (included with Invitrogen #18080-044), 3 μl 0.1 M DTT (included with Invitrogen #18080-044), 0.6 μl 25 mM dNTP’s (Invitrogen #10297-018)/aa-dUTP (2:3 aa-dUTP (Ambion #8439) to dTTP) labeling mix, and 2.0 μl Superscript III reverse transcriptase (200U/μl) (Invitrogen #18080-044). 4. Mix and incubate in a 42°C water bath overnight. 5. Hydrolyze RNA strand by adding 10 μl of 0.5 M EDTA and 10 μl of 1.0 M NaOH 6. Mix and incubate at 65°C for 15 minutes. 7. Add 25 μl of 1.0 M Tris (pH 7.0) to neutralize pH. Part 2: 1. Clean-up reactions using Qiagen MinElute columns (Qiagen #28004). 2. Mix each reaction with 400 μl of PB buffer (included in Qiagen #28004) and transfer to MinElute columns. 3. Centrifuge at 13,000 rpm for 1 min and discard flow through. 4. Wash with 750 μl of phosphate wash buffer (5 mM KPO4 pH 8.0 and 80% ethanol) and centrifuge at 13,000 rpm for 1 minute. 5. Discard flow through and centrifuge an additional minute at 13,000 rpm. 6. Transfer column to a new 1.5 ml centrifuge tube and add 30 μl of phosphate elution buffer (4 mM KPO4 pH 8.5). 7. Let sit at room temperature for 1 min and centrifuge for 1 min at 13,000 rpm. 8. Add another 30 μl of phosphate elution buffer and repeat elution step 7. 9. Transfer open tubes to speed vac and dry on high heat for about 20-30 min. 10. Let 4.5 μl of 0.1 M sodium carbonate buffer pH 9.3 (made fresh) sit on pellet for 10-15 minutes. Resuspend by pipeting slowly for 2-3 minutes. 11. Add 4.5 μl Cy3 (Amersham Biosciences #PA23001) 12. Incubate at room temperature in the dark for 2 hr. 13. Clean up reactions using Qiagen MinElute columns. 14. Mix samples with 250 μl of PB buffer and transfer to MinElute column. 15. Centrifuge at 13,000 rpm for 1 min, and discard flow through. 16. Wash with 750 μl of PE buffer (included in Qiagen #28004) and centrifuge at 13,000 rpm for 1 min. 17. Discard flow through, and transfer to a new 1.5 microfuge tube and add 50 μl of DI water. 18. Let samples sit at room temperature for 1 min and spin at 13,000 rpm for 1 min. 19. Add another 50 μl of DI water and repeat elution step 18. 20. Mix labeled probes and dry down in speed vac on high heat for about 30-40 minutes.

growth_protocol: Cells were grown overnight in LB at 37°C with shaking, subcultured into LB and grown to log phase at 37°C with shaking.

extract_protocol: Hot phenol/chloroform extract of total RNA: 1. Place 25.0 ml of phenol (Sigma, P4682-400mL) into a glass bottle, cap bottle loosely. Never use ddH20, only use DI water for all array protocols. 2. Place bottle of phenol in boiling water 100°C. 3. Heat phenol for approximately 10 minutes prior to extraction. 4. Transfer 25.0 ml of a bacterial culture into the hot phenol. 5. Shake to mix the phases. 6. Loosen cap every so often to release gas build up. 7. Heat for about 15-30 minutes. The mixture should look like one layer, not two. 8. Transfer mixtures into two “RNase-treated” centrifuge tubes (Ambion). 9. Place tubes on ice. 10. Add 5.0 ml of chloroform to each tube. 11. Mix thoroughly and release gas build up. 12. Spin at 10,000 g at 4°C for 10 minutes. 13. Transfer aqueous phases (top layer) to a fresh centrifuge tube. Be careful not to get bottom layer of debris; this will ruin the quality of the RNA. Instead, leave 1-3 mls of the aqueous layer behind. 14. Add 6.25 ml of phenol to each tube. 15. Add 6.25 ml of chloroform to each tube. 16. Shake to mix and release gas build up. 17. Spin at 10,000 g at 4°C for 10 minutes. 18. Transfer each aqueous phase (top layer) to a fresh centrifuge tube. Be careful not to get bottom layer of debris; this will ruin the quality of the RNA. 19. Add 0.1 volume of 3.0 M sodium acetate in DEPC (diethylpyrocarbonate) treated water (Ambion) to each of the tubes. 20. Add an equal volume of isopropanol to each tube. 21. Cool on ice for 30 minutes. Longer incubations do not increase RNA yield. 22. Spin at 10,000 g at 4°C for 60 minutes. Longer spins will increase RNA yield. 21. Remove all of the supernatant, pat inverted tubes onto paper towels to remove excess supernatant being careful not to contaminate RNA or lose RNA pellet, then allow the pellet to air dry upright in uncapped tubes for 5 minutes in the fume hood. 23. Resuspend the pellet in RNase free water containing 200 U/ml RNaseOUT (Invitrogen).

tag: Strain

label_protocol: Part 1: 1. Using RNase free tubes, mix: 1.5 μg of genomic DNA, 3.3 ul random hexamers (3 mg/ml) (Invitrogen #48190-011), and bring to 39 μl with DI water. 2. Mix well and incubate at 100°C for 12 min. 3. Snap-freeze in dry ice/ethanol bath for 30 sec, centrifuge briefly, and bring to room temperature. 4. Mix: 39 μl of above genomic DNA/primer mix, 5 μl of 10X EcoPol (Klenow) buffer (included with New England Biolabs #M0212L), 2 μl of 5 mM dNTP’s (Invitrogen #10297-018)/aa-dUTP (2:3 aa-dUTP (Ambion #8439) to dTTP) labeling mix, and 4 μl DNA Polymerase I Klenow fragment (New England Biolabs #M0212L). 5. Mix and incubate at 37°C overnight. 6. Stop reaction by adding 5 μl of 0.5 M EDTA (pH 8.0). Part 2: 1. Clean-up reactions using Qiagen MinElute columns (Qiagen #28004). 2. Mix each reaction with 400 μl of PB buffer (included in Qiagen #28004) and transfer to MinElute columns. 3. Centrifuge at 13,000 rpm for 1 min and discard flow through. 4. Wash with 750 μl of phosphate wash buffer (5 mM KPO4 pH 8.0 and 80% ethanol) and centrifuge at 13,000 rpm for 1 minute. 5. Discard flow through and centrifuge an additional minute at 13,000 rpm. 6. Transfer column to a new 1.5 ml centrifuge tube and add 30 μl of phosphate elution buffer (4 mM KPO4 pH 8.5). 7. Let sit at room temperature for 1 min and centrifuge for 1 min at 13,000 rpm. 8. Add another 30 μl of phosphate elution buffer and repeat elution step 7. 9. Transfer open tubes to speed vac and dry on high heat for about 20-30 min. 10. Let 4.5 μl of 0.1 M sodium carbonate buffer pH 9.3 (made fresh) sit on pellet for 10-15 minutes. Resuspend by pipeting slowly for 2-3 minutes. 11. Add 4.5 μl Cy5 dye (Amersham Biosciences #PA25001). 12. Incubate at room temperature in the dark for 2 hr. 13. Clean up reactions using Qiagen MinElute columns. 14. Mix samples with 250 μl of PB buffer and transfer to MinElute column. 15. Centrifuge at 13,000 rpm for 1 min, and discard flow through. 16. Wash with 750 μl of PE buffer (included in Qiagen #28004) and centrifuge at 13,000 rpm for 1 min. 17. Discard flow through, and transfer to a new 1.5 microfuge tube and add 50 μl of DI water. 18. Let samples sit at room temperature for 1 min and spin at 13,000 rpm for 1 min. 19. Add another 50 μl of DI water and repeat elution step 18. 20. Mix labeled probes and dry down in speed vac on high heat for about 30-40 minutes.

growth_protocol: Cells were grown overnight in LB at 37°C with shaking.

extract_protocol: Genomic DNA was extracted using a GenElute kit (Sigma )


title: wild type array 3 subarray 2


title: wild type array 2 subarray 2


title: wild type array 1 subarray 3


title: wild type array 1 subarray 2


title: wild type array 2 subarray 1


title: wild type array 1 subarray 1


title: corA mutant array 3 subarray 3

source_name: corA mutant

growth_protocol: Cells were grown overnight in LB with antibiotics at 37°C with shaking, subcultured into LB without antibiotics and grown to log phase at 37°C with shaking.

tag: Mutations

value: corA::Tn10 (tet)


title: corA mutant array 3 subarray 2


title: corA mutant array 3 subarray 1


title: corA mutant array 2 subarray 3


title: corA mutant array 1 subarray 2

hyb_protocol: Prepping slides for hybridization: 1. Warm up slide pre-hybridiztion solution (25% formamide, 5X SSC (Ambion #9763), 0.1% SDS, 0.1 mg/ml BSA) to 42°C in a Coplin jar (VWR# 25457-200) in a water bath. 2. Incubate microarray slides in pre-warmed hybridization solution for 60 min at 42°C. 3. Wash arrays 10X in glass Wheaton dishes (Wheaton Science Products #900200) with DI water. 4. Wash arrays 1X with isopropanol. 5. Dry arrays by centrifugation at 1000 rpm for 15-20 min. 6. Make hybridization buffer: 250 μl of formamide, 250 μl of 20X SSC, 490 μl of DI water, and add 10 μl 10% SDS last. Filter hybridization buffer with a 0.45 μm filter. 7. Heat probe at 95°C on heat block for 5-10 min and vortex to resuspend. 8. Warm up hybridization chambers (Corning #2551) with slides inside on heat block. 9. Add hot probe to center of hot slide. Hold cover slip at 45° angle close to slide surface and drop. Add hybridization buffer to the bottom of the chamber to keep it humidified. 10. Close up chambers, cover with foil, weigh down in 42°C water bath, and incubate overnight. Post-Hybridization and scanning: 1. Remove cover slips by holding slides upside down in warm (55°C) low stringency buffer (2X SSC and 0.1% SDS in dH20) in a large glass dish. Remove fallen cover slip and wash slides vigorously in large glass dish for 2-3 min. Then wash 2 times for 5 min with warm (55°C) low stringency buffer (2X SSC and 0.1% SDS in dH20) in Wheaton dish on an orbital shaker  Do not let slides dry out during washing process. 2. Wash slides vigorously 2 times for 5 min with room temperature medium stringency buffer (0.1X SSC and 0.1% SDS in dH20). 3. Wash slides vigorously 2 times for 5 min with room temperature high stringency buffer (0.1X SSC in dH20). 4. Wash slides in water 1 time for 3 min and transfer to centrifuge. 5. Dry slides by centrifugation for 15-20 min at 1000 rpm. 6. Slides should be kept in the dark until they are scanned.


title: corA mutant array 1 subarray 3


title: wild type array 2 subarray 3


title: corA mutant array 2 subarray 1


title: wild type array 3 subarray 3


title: corA mutant array 1 subarray 1

hyb_protocol: Prepping slides for hybridization: 1.  Warm up slide pre-hybridiztion solution (25% formamide, 5X SSC (Ambion #9763), 0.1% SDS, 0.1 mg/ml BSA) to 42°C in a Coplin jar (VWR# 25457-200) in a water bath. 2.  Incubate microarray slides in pre-warmed hybridization solution for 60 min at 42°C. 3.  Wash arrays 10X in glass Wheaton dishes (Wheaton Science Products #900200) with DI water. 4.  Wash arrays 1X with isopropanol. 5.  Dry arrays by centrifugation at 1000 rpm for 15-20 min. 6.  Make hybridization buffer:  250 μl of formamide, 250 μl of 20X SSC, 490 μl of DI water, and add 10 μl 10% SDS last.   Filter hybridization buffer with a 0.45 μm filter. 7.  Heat probe at 95°C on heat block for 5-10 min and vortex to resuspend. 8.  Warm up hybridization chambers (Corning #2551) with slides inside on heat block. 9.  Add hot probe to center of hot slide.  Hold cover slip at 45° angle close to slide surface and drop.  Add hybridization buffer to the bottom of the chamber to keep it humidified. 10.  Close up chambers, cover with foil, weigh down in 42°C water bath, and incubate overnight. Post-Hybridization and scanning: 1.  Remove cover slips by holding slides upside down in warm (55°C) low stringency buffer (2X SSC and 0.1% SDS in dH20) in a large glass dish.  Remove fallen cover slip and wash slides vigorously in large glass dish for 2-3 min.  Then wash 2 times for 5 min with warm (55°C) low stringency buffer (2X SSC and 0.1% SDS in dH20) in Wheaton dish on an orbital shaker.  Do not let slides dry out during washing process. 2.  Wash slides vigorously 2 times for 5 min with room temperature medium stringency buffer (0.1X SSC and 0.1% SDS in dH20). 3.  Wash slides vigorously 2 times for 5 min with room temperature high stringency buffer (0.1X SSC in dH20). 4.  Wash slides in water 1 time for 3 min and transfer to centrifuge. 5.  Dry slides by centrifugation for 15-20 min at 1000 rpm.  6.  Slides should be kept in the dark until they are scanned.

scan_protocol: Slides were scanned using a GenePix 4000B microarray scanner.  Slides should be scanned to obtain a ratio between 0.8-1.2 for Cy3/Cy5 fluorescence.

label_protocol:
Part 1:
1.  Using RNase free tubes, mix:  30 μg of total RNA, 2 μl  random hexamers (3 mg/ml) (Invitrogen #48190-011), 1 μl RNaseOUT (Invitrogen #10777-019), and bring to 18.5 μl with DEPC water.
2.  For RNA labeling, mix well, incubate at 70°C for 10 min, snap freeze in a dry ice/ethanol bath for 30 sec, centrifuge briefly, and bring to room temperature.
3.  Mix the following:  18.5 μl of RNA/primer mix from above step, 6 μl 5X first strand buffer (included with Invitrogen #18080-044),  3 μl 0.1 M DTT (included with Invitrogen #18080-044), 0.6 μl  25 mM dNTP’s (Invitrogen #10297-018)/aa-dUTP (2:3 aa-dUTP (Ambion #8439) to dTTP) labeling mix, and 2.0 μl Superscript III reverse transcriptase (200U/μl) (Invitrogen #18080-044).
4.  Mix and incubate in a 42°C water bath overnight.
5.  Hydrolyze RNA strand by adding 10 μl of 0.5 M EDTA and 10 μl of 1.0 M NaOH
6.  Mix and incubate at 65°C for 15 minutes.
7.  Add 25 μl of 1.0 M Tris (pH 7.0) to neutralize pH.
Part 2:
1.  Clean-up reactions using Qiagen MinElute columns (Qiagen #28004).
2.  Mix each reaction with 400 μl of PB buffer (included in Qiagen #28004) and transfer to MinElute columns.
3.  Centrifuge at 13,000 rpm for 1 min and discard flow through.
4.  Wash with 750 μl of phosphate wash buffer (5 mM KPO4 pH 8.0 and 80% ethanol) and centrifuge at 13,000 rpm for 1 minute.
5.  Discard flow through and centrifuge an additional minute at 13,000 rpm.
6.  Transfer column to a new 1.5 ml centrifuge tube and add 30 μl of phosphate elution buffer (4 mM KPO4 pH 8.5).
7.  Let sit at room temperature for 1 min and centrifuge for 1 min at 13,000 rpm.
8.  Add another 30 μl of phosphate elution buffer and repeat elution step 7.
9.  Transfer open tubes to speed vac and dry on high heat for about 20-30 min.
10.  Let 4.5 μl of 0.1 M sodium carbonate buffer pH 9.3 (made fresh) sit on pellet for 10-15 minutes.  Resuspend by pipeting slowly for 2-3 minutes.
11.  Add 4.5 μl Cy3 (Amersham Biosciences #PA23001)
12.  Incubate at room temperature in the dark for 2 hr.
13.  Clean up reactions using Qiagen MinElute columns.
14.  Mix samples with 250 μl of PB buffer and transfer to MinElute column.
15.  Centrifuge at 13,000 rpm for 1 min, and discard flow through.
16.  Wash with 750 μl of PE buffer (included in Qiagen #28004) and centrifuge at 13,000 rpm for 1 min.
17.  Discard flow through, and transfer to a new 1.5 microfuge tube and add 50 μl of DI water.
18.  Let samples sit at room temperature for 1 min and spin at 13,000 rpm for 1 min.
19.  Add another 50 μl of DI water and repeat elution step 18.
20.  Mix labeled probes and dry down in speed vac on high heat for about 30-40 minutes.

extract_protocol:
Hot phenol/chloroform extract of total RNA:
1.  Place 25.0 ml of phenol (Sigma, P4682-400mL) into a glass bottle, cap bottle loosely.  Never use ddH20, only use DI water for all array protocols.
2.  Place bottle of phenol in boiling water 100°C.
3.  Heat phenol for approximately 10 minutes prior to extraction.
4.  Transfer 25.0 ml of a bacterial culture into the hot phenol.
5.  Shake to mix the phases.
6.  Loosen cap every so often to release gas build up.
7.  Heat for about 15-30 minutes.  The mixture should look like one layer, not two.
8.  Transfer mixtures into two “RNase-treated” centrifuge tubes (Ambion).
9.  Place tubes on ice.
10.  Add 5.0 ml of chloroform to each tube.
11.  Mix thoroughly and release gas build up.
12.  Spin at 10,000 g at 4°C for 10 minutes.
13.  Transfer aqueous phases (top layer) to a fresh centrifuge tube.  Be careful not to get bottom layer of debris; this will ruin the quality of the RNA.   Instead, leave 1-3 mls of the aqueous layer behind.
14.  Add 6.25 ml of phenol to each tube.
15.  Add 6.25 ml of chloroform to each tube.
16.  Shake to mix and release gas build up.
17.  Spin at 10,000 g at 4°C for 10 minutes.
18.  Transfer each aqueous phase (top layer) to a fresh centrifuge tube.  Be careful not to get bottom layer of debris; this will ruin the quality of the RNA.
19.  Add 0.1 volume of 3.0 M sodium acetate in DEPC (diethylpyrocarbonate) treated water (Ambion) to each of the tubes.
20.  Add an equal volume of isopropanol to each tube.
21.  Cool on ice for 30 minutes.  Longer incubations do not increase RNA yield.
22.  Spin at 10,000 g at 4°C for 60 minutes.  Longer spins will increase RNA yield.
21.  Remove all of the supernatant, pat inverted tubes onto paper towels to remove excess supernatant being careful not to contaminate RNA or lose RNA pellet, then allow the pellet to air dry upright in uncapped tubes for 5 minutes in the fume hood.
23.  Resuspend the pellet in RNase free water containing 200 U/ml RNaseOUT (Invitrogen).

label_protocol:
Part 1:
1.  Using RNase free tubes, mix:  1.5 μg of genomic DNA, 3.3 ul random
hexamers (3 mg/ml) (Invitrogen #48190-011), and bring to 39 μl with DI water.
2.  Mix well and incubate at 100°C for 12 min.
3.  Snap-freeze in dry ice/ethanol bath for 30 sec, centrifuge briefly, and bring to room temperature.
4.  Mix:  39 μl of above genomic DNA/primer mix, 5 μl of 10X EcoPol (Klenow) buffer (included with New England Biolabs #M0212L), 2 μl of 5 mM dNTP’s (Invitrogen #10297-018)/aa-dUTP (2:3 aa-dUTP (Ambion #8439) to dTTP) labeling mix, and 4 μl DNA Polymerase I Klenow fragment (New England Biolabs #M0212L).
5.  Mix and incubate at 37°C overnight.
6.  Stop reaction by adding 5 μl  of 0.5 M EDTA (pH 8.0).
Part 2:
1.  Clean-up reactions using Qiagen MinElute columns (Qiagen #28004).
2.  Mix each reaction with 400 μl of PB buffer (included in Qiagen #28004) and transfer to MinElute columns.
3.  Centrifuge at 13,000 rpm for 1 min and discard flow through.
4.  Wash with 750 μl of phosphate wash buffer (5 mM KPO4 pH 8.0 and 80% ethanol) and centrifuge at 13,000 rpm for 1 minute.
5.  Discard flow through and centrifuge an additional minute at 13,000 rpm.
6.  Transfer column to a new 1.5 ml centrifuge tube and add 30 μl of phosphate elution buffer (4 mM KPO4 pH 8.5).
7.  Let sit at room temperature for 1 min and centrifuge for 1 min at 13,000 rpm.
8.  Add another 30 μl of phosphate elution buffer and repeat elution step 7.
9.  Transfer open tubes to speed vac and dry on high heat for about 20-30 min.
10.  Let 4.5 μl of 0.1 M sodium carbonate buffer pH 9.3 (made fresh) sit on pellet for 10-15 minutes.  Resuspend by pipeting slowly for 2-3 minutes.
11.  Add 4.5 μl Cy5 dye (Amersham Biosciences #PA25001).
12.  Incubate at room temperature in the dark for 2 hr.
13.  Clean up reactions using Qiagen MinElute columns.
14.  Mix samples with 250 μl of PB buffer and transfer to MinElute column.
15.  Centrifuge at 13,000 rpm for 1 min, and discard flow through.
16.  Wash with 750 μl of PE buffer (included in Qiagen #28004) and centrifuge at 13,000 rpm for 1 min.
17.  Discard flow through, and transfer to a new 1.5 microfuge tube and add 50 μl of DI water.
18.  Let samples sit at room temperature for 1 min and spin at 13,000 rpm for 1 min.
19.  Add another 50 μl of DI water and repeat elution step 18.
20.  Mix labeled probes and dry down in speed vac on high heat for about 30-40 minutes.


title: corA mutant array 2 subarray 2


title: Naive+ GPN L4 DRG,Contra set B

description: Gene expression data


title: Naive sc, contra set B

description: Gene expression data


title: L139

status: Public on Mar 01 2008

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68232.gif
Cell Line: L139
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.

hyb_protocol: not provided

scan_protocol: not provided

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

source_name: Normal human male genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Normal human male genomic DNA


title: L223

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68233.gif
Cell Line: L223
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.


title: L44

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68230.gif
Cell Line: L44
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.


title: H661

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62919.gif
Cell Line: H661
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.


title: HBEC2-KT

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49595.gif
Cell Line: HBEC2-KT
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.

source_name: HBEC2-KT; immortalized (8641)

tag: HBEC2-KT; immortalized (8641)


title: H322

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62917.gif
Cell Line: H322
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.


title: Normal

description:
Simple annotation: X Chromosome, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44540.gif
Cell Line: normal
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.

source_name: Normal female genomic DNA

tag: Normal female genomic DNA

source_name: Normal; NM vs. NF

tag: Normal; NM vs. NF


title: L222

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs//68231.gif
Cell Line: L222
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.


title: HBEC4-KT

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49592.gif
Cell Line: HBEC4-KT
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.

source_name: Normal human female genomic DNA

tag: Normal human female genomic DNA

source_name: HBEC4-KT; immortalized (8643)

tag: HBEC4-KT; immortalized (8643)


title: HBEC5-KT

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49593.gif
Cell Line: HBEC5-KT
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.

source_name: HBEC5-KT; immortalized (8644)

tag: HBEC5-KT; immortalized (8644)


title: H2882_RNA

description:
NHBEC, SAEC and BEAS-2B are Normal lung epithelial cell lines, the others are Lung cancer cell lines
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24834.gif
Cell Line: H2882

source_name: Common reference, CRH

tag: Common reference, CRH


title: CaLu-3

description:
Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62330.gif
Cell Line: CaLu-3
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.

source_name: Normal male human genomic DNA

tag: Normal male human genomic DNA

source_name: CaLu-3; AD (GD158s1)

tag: CaLu-3; AD (GD158s1)