title: CaCo2_TNF_60min_rep8

city: Rostock

first: Hermann

last: Schulze

address: Ernst-Heydemann-Str. 6

institute: Universitätsklinik Rostock

description: Comparison of gene expression patterns of TNF-alpha stimulated and not stimulated CaCo-2 cells

hyb_protocol: Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C. These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction. Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm). The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL). The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C. Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C. Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.

scan_protocol: Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan).

data_processing: The image data files were gridded using AIDA software (Raytest, Straubenhardt, Germany) and the results were imported in a custom-made database. The ranked expression data distribution was found to follow Zipf´s law (Hoyle et al, 2002) and the logarithmic normal transformed datasets were normalised following this principle, as previously described by Lu et al. 2005. Any hybridisation signal that had a value that fell below a predefined threshold (mean background + 2x standard deviation) were considered as indistinguishable from background and was set to zero. Those values where duplicate expression values for the same gene were not similar (outliers or false positive, difference between duplicates >20%) were eliminated.

label: α33P-dCTP random hexamer labeling

source_name: CaCo-2 cell line

label_protocol: 200 - 500 ng mRNA was isolated from total RNA sample using the Oligotex kit (Qiagen) according to the manufacturer’s instructions. Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983). Reversed transcribed cDNA were prepared in a final volume of 30microL as described in detail previously (labeling reaction at 42°C for 60 min; Eickhoff et al. 2000). RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl. Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).

growth_protocol: The cells were cultured in DMEM containing 20% foetal bovine serum, 100 U/ml penicillin and 100 ng/ml streptomycin. Before passaging, the adherent cells were rinsed with PBS (37°C) three times to remove the fetal bovine serum that inhibits the trypsinization and trypsinized with 5-8 ml of Trypsine/EDTA solution at 37°C in the incubator. Confluent cell cultures (3-6 x 105 cells/cm2) were split, and seeded out for stimulation at 1 x 105 cells/cm2.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol, with minor modifications that improved RNA yields and purity in our hands. Cells were lysed in an appropriate volume of Buffer RLT. To facilitate complete lysis, samples were allowed to stand at room temperature for 5-10 min before vortexing. The lysate was homogenized by addition to a QIA shredder column (Qiagen) and centrifuged at 14,000 rpm for 2 min. The resulting supernatant was centrifuged at 14,000 rpm for 3 min to pellet any cell debris. One volume of 70% ethanol was added to the cleared lysate, added to the RNeasy column and centrifuged at 10,000 rpm for 15 sec. Bound RNA was washed with the addition of RW1 buffer to the column and allowed to stand at room temperature for 10 min followed by centrifugation at 10,000 rpm for 15 sec. DNase 1 incubation mix (Stock: 273 kunits; RNase-free DNase Set, Qiagen) was added directly to the spin column membrane and digestion of any contaminating genomic DNA was carried out at room temperature for 30 min. The column was washed with RWI buffer and the DNase treatment step was repeated. The bound RNA was washed with RW1 buffer and centrifuged at 10,000 rpm for 15 sec three times, followed by two additional wash and centrifugation steps with RPE buffer. Finally, purified RNA was eluted off the column with RNase-free water. RNA concentration and purity was determined spectrophotometrically at A260/A280 and was determined to be intact as assessed by formaldehyde gel electrophoresis. The presence of genomic DNA contamination was assessed by PCR amplification of GAPDH using standard PCR conditions and the following primers: GAPDH_F2-5’- ACCCACTCCTCCACCTTTGAC-3’, GAPDH_R2- 5’-CTGTTGCTGTAGCCAAATTCGT-3’. RNA was re-treated with DNase if necessary. Upon confirming the quality of the RNA (intact and free of genomic DNA), 15 µg of total RNA for expression screening.

treatment_protocol: Cells were stimulated for 60 min with recombinant human TNF-α in a final concentration of 5 ng/ml.

tag: epithelial adherent cell line established from a human colon adenocarcinoma


title: CaCo2_TNF_60min_rep5

status: Public on Feb 29 2008

type: RNA

country: Germany

molecule: total RNA

organism: Homo sapiens


title: CaCo2_TNF_60min_rep3


title: CaCo2_TNF_60min_rep2


title: CaCo2_TNF_60min_rep7


title: CaCo2_TNF_60min_rep6


title: CaCo2_TNF_60min_rep4


title: CaCo2_control_rep5


title: CaCo2_control_rep9


title: CaCo2_control_rep6


title: CaCo2_control_rep10


title: THP1_TNF_60min_rep6

description: Comparison of gene expression patterns of TNF-alpha stimulated and not stimulated THP-1 cells

source_name: THP-1 cell line

growth_protocol: The cells were cultured in RPMI 1640 containing 2 mM L-glutamine and 10% fetal bovine serum (inactivated by incubation at 56°C for at least 30 min prior to use) supplemented with 0.05 mM 2-mercaptoethanol, 100 U/ml penicillin and 100 ng/ml streptomycin. Subculturing was performed by splitting and diluting cells when the concentration exceeded 1 x 106 cells/ml. Cell concentrations were determined using a Neubauer chamber and cells were stimulated in cell culture dishes (10 cm diameter) in 10 ml of medium and a cell concentration of 0.5 x 106 cells/ml.

tag: cell line derived from an acute monocytic leukaemia patient


title: CaCo2_control_rep1


title: THP1_TNF_60min_rep8


title: CaCo2_control_rep8


title: CaCo2_control_rep4


title: THP1_TNF_60min_rep5


title: CaCo2_control_rep2


title: CaCo2_control_rep3


title: CaCo2_TNF_60min_rep1


title: CaCo2_control_rep7


title: THP1_TNF_60min_rep1


title: THP1_TNF_60min_rep7


title: THP1_TNF_60min_rep3


title: THP1_TNF_60min_rep4


title: THP1_control_rep7


title: THP1_TNF_60min_rep2


title: THP1_control_rep5


title: THP1_control_rep6


title: THP1_control_rep3


title: THP1_control_rep4


title: THP1_control_rep2


title: Lung cancer metastatic gene signature: metastatic cell line M5, bio-replicate 3.

status: Public on Feb 15 2008

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description:
Human highly metastatic cell line M5. Bio-Replicate 3.
(28-metM5+)

hyb_protocol: Standard hybridization protocol for Affymetrix GeneChips

scan_protocol: Standard scan protocol for Affymetrix GeneChips

data_processing: RMA, SAM, hclust using R and Bioconductor

label: Standard label for Affymetrix GeneChips

label_protocol: Standard mRNA label protocol for Affymetrix GeneChips

extract_protocol: Standard mRNA extraction protocol for Affymetrix GeneChips

tag: Human highly metastatic cell lines derived from Non-Small Cell Lung Carcinoma (NSCLC) with specific bone tropism. Cell lines were stably transfected with a luciferase reporter gene. During screening, selected cell lines induced prominent bone metastases lesions in the hind limbs.

tag: Subpopulations of cells with high metastatic ability were isolated using the following strategy

value: after intracardiac (i.c.) injection of control cells, the subpopulations metastasizing with a high efficiency to bone were isolated and metastatic activity for each one was assessed by i.c. reinoculation of 10 mice per group. With some subpopulations, bone metastases appeared with a latency time ranging from 9-15 days to 20-30 days.

tag: To assess the metastatic activity and to be able to systematically and accurately discriminate the subpopulations with different metastatic activities three complementary parameters were evaluated. First, metastatic activity of the injected control cells and all derived cellular subpopulations was assessed using Kaplan-Meier curves. Compared to the control cell line, several subpopulations named M1, M4 and M5 had an increased metastatic activity by thriving efficiently at bone and decreasing animal survival. Second, 22 days post-inoculation, computerized image analysis revealed an increased bone metastatic area of the hind limbs induced by the more aggressive subpopulations M1, M4 and M5 compared to the control cell lines. And third, 22 days after i.c. inoculation, metastatic cells in the hind limbs were isolated by bone marrow “flushing”. Conspicuous SCCs derived from each animal (10 mice/group) were counted. Subpopulations M1, M4 and M5 induced a more abundant yield of SCCs than control cell lines.


title: Lung cancer metastatic gene signature: metastatic cell line M5, bio-replicate 2.

description:
Human highly metastatic cell line M5. Bio-Replicate 2.
(27-metM5+)

source_name: Human highly metastatic cell lines derived from Non-Small Cell Lung Carcinoma (NSCLC)


title: VAP_patient1_time19

status: Public on Feb 12 2008

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

country: USA

institute: Washington University in St. Louis

description: Gene expression data (Affy Chip Hg-Focus)

hyb_protocol: 10 micrograms cRNA was hybed for 16 hours at 45 degrees on the Affymetrix Human Genome Focus Arrays.  The washes and stains wee done on the Affymetrix’s GeneChip Fluidics Station 450 with program Midi_euk2v3.

scan_protocol: Gene Chips were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed (including normalization and modelling) with RMA

label: biotin

label_protocol: Biotintalated cRNA was prepared from 2 micrograms RNA using Affymetrix’s IVT labeling kit using, in accordance with the Trauma Glue Grant’s G007.09 protocol (www.gluegrant.org)

extract_protocol: Circulating white blood cells were recovered from blood following the Trauma Glue Grant protocol G025.09 (www.gluegrant.org).  The RNA was then extracted from leukocytes using the RNeasy Midi columns.

tag: Tissue

value: Blood

tag: VAP

value: Day 6

tag: Gender

value: Male

tag: Age

tag: Ethnicity

value: Caucasian

tag: Infecting Organism

value: Serratia marcescens (gram negative)


title: Lung cancer metastatic gene signature: metastatic cell line M1, bio-replicate 1.

description:
Human highly metastatic cell line M1. Bio-Replicate 1.
(16-metM1+)


title: Lung cancer metastatic gene signature: metastatic cell line M1, bio-replicate 2.

description:
Human highly metastatic cell line M1. Bio-Replicate 2.
(22-metM1+)


title: Lung cancer metastatic gene signature: metastatic cell line M4, bio-replicate 2.

description:
Human highly metastatic cell line M4. Bio-Replicate 2.
(24-metM4+)


title: VAP_patient1_time17


title: VAP_patient1_time15


title: Lung cancer metastatic gene signature: metastatic cell line M1, bio-replicate 3.

description:
Human highly metastatic cell line M1. Bio-Replicate 3.
(26-metM1+)


title: Lung cancer metastatic gene signature: control cell lines with luciferase reporter, bio-replicate 2.

description:
Control cell lines with luciferase reporter. Biological replicate 2.
(14-ctrSiLuc)


title: VAP_patient1_time9


title: Lung cancer metastatic gene signature: metastatic cell line M4, bio-replicate 1.

description:
Human highly metastatic cell line M4. Bio-Replicate 1.
(18-metM4+)


title: VAP_patient1_time7


title: VAP_patient1_time13


title: Lung cancer metastatic gene signature: control cell lines without luciferase reporter, bio-replicate 2.

description:
Control cell lines without luciferase reporter. Biological replicate 2.
(13-ctrNoLuc)


title: Lung cancer metastatic gene signature: metastatic cell line M5, bio-replicate 1.

description:
Human highly metastatic cell line M5. Bio-Replicate 1.
(21-metM5+)


title: Lung cancer metastatic gene signature: control cell lines with luciferase reporter, bio-replicate 1.

description:
Control cell lines with luciferase reporter. Biological replicate 1.
(12-ctrSiLuc)


title: Lung cancer metastatic gene signature: metastatic cell line M4, bio-replicate 3.

description:
Human highly metastatic cell line M4. Bio-Replicate 3.
(25-metM4+)


title: VAP_patient1_time3


title: VAP_patient1_time5


title: VAP_patient1_time1


title: VAP_patient2_time17

value: Acinetobacter calcoaceticus-baumanii & Serratia marcescens (Gram negative)


title: VAP_patient2_time19


title: VAP_patient2_time13


title: VAP_patient1_time11


title: VAP_patient2_time11


title: Lung cancer metastatic gene signature: control cell lines without luciferase reporter, bio-replicate 1.

description:
Control cell lines without luciferase reporter. Biological replicate 1.
(11-ctrNoLuc)


title: VAP_patient2_time3


title: VAP_patient2_time5


title: VAP_patient2_time7


title: VAP_patient3_time11

value: Day 4

value: Enterobacter aerogenes (Gram Negative)


title: VAP_patient3_time7


title: VAP_patient3_time9


title: VAP_patient3_time13


title: VAP_patient2_time1


title: VAP_patient5_time21

value: Day 3

value: Female

value: Staphylococcus aureus (Gram Positive)


title: VAP_patient5_time19


title: VAP_patient3_time3


title: VAP_patient5_time15


title: VAP_patient5_time9


title: VAP_patient3_time5


title: VAP_patient5_time17


title: VAP_patient2_time9


title: VAP_patient5_time11


title: VAP_patient5_time5


title: VAP_patient5_time7


title: VAP_patient3_time15


title: VAP_patient5_time1


title: VAP_patient5_time3


title: VAP_patient7_time21

value: African American

value: Stenotrophomonas maltophilia (Gram Negative)


title: VAP_patient5_time13


title: VAP_patient7_time17


title: VAP_patient7_time9


title: THP1_control_rep1


title: VAP_patient7_time11


title: VAP_patient7_time7


title: VAP_patient7_time13


title: VAP_patient7_time5


title: VAP_patient7_time1


title: VAP_patient9_time7


title: VAP_patient7_time15


title: VAP_patient7_time19


title: VAP_patient9_time9


title: VAP_patient7_time3


title: VAP_patient9_time5


title: VAP_patient9_time3


title: VAP_patient10_time19

value: Day 19

tag: Infecting Organism:3-Pantoea (enterobacter) agglomerans; 19-Stenotrophomonas maltophilia and Pseudomonas aeruginosa (Gram Negative)


title: VAP_patient9_time1


title: VAP_patient10_time21


title: VAP_patient10_time17


title: VAP_patient10_time9


title: VAP_patient10_time11


title: VAP_patient10_time13


title: VAP_patient10_time15


title: VAP_patient10_time5


title: VAP_patient11_time11

value: Day 5

value: Acinetobacter calcoaceticus-baumanii (Gram Negative)


title: VAP_patient10_time1


title: VAP_patient11_time13


title: VAP_patient10_time3


title: VAP_patient10_time7


title: VAP_patient18_time19

value: Escerischia coli, Haemophilus influenzae and Streptococcus pneumoniae (Mixed Gram Positive and Negative)


title: VAP_patient11_time3

value: Blood


title: VAP_patient11_time5


title: VAP_patient18_time15

value: Day 6


title: VAP_patient11_time7


title: VAP_patient18_time21


title: VAP_patient18_time17


title: VAP_patient11_time9


title: VAP_patient18_time7


title: VAP_patient18_time5


title: VAP_patient18_time1


title: VAP_patient11_time1


title: VAP_patient22_time13

value: Haemophilus influenzae (Gram Negative)


title: VAP_patient18_time13

value: Caucasian


title: VAP_patient3_time1

value: Male


title: VAP_patient29_time21

value: Day 14


title: VAP_patient22_time7


title: VAP_patient22_time9


title: VAP_patient29_time15


title: VAP_patient18_time3


title: VAP_patient22_time1


title: VAP_patient29_time19


title: VAP_patient29_time7


title: VAP_patient22_time5


title: VAP_patient18_time9


title: VAP_patient22_time17


title: VAP_patient22_time3


title: VAP_patient29_time13


title: VAP_patient29_time9


title: Comparison -2.5°C versus 10°C - Replicate 3

status: Public on Feb 11 2008

city: East Lansing

first: Debora

middle: Frigi

last: Rodrigues

state: MI

address: 540 Plant and Soil Science Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: Biological replicate 6 of 6 and dye swap

hyb_protocol: Microarray slides were incubated for 60 min at 46°C with prehybridization solution (50% Ultrapure formamide (Invitrogen), 5x SSC, 0.1% SDS and 0.1 mg ml-1), washed three times in double-distilled water and one time in isopropanol, and dried by centrifugation at 50 X g for 3 min. Two cDNA's from different temperatures were mixed for direct comparisons for all temperature combinations. Each microarray received about 30 ul of hybridization solution (50% Ultrapure Formamide, 5x SSC, 0.1% SDS, 0.1 ug/ul Salmon sperm DNA) containing the two cDNAs. The solution was applied by capillary action under a coverslip (LifterSlip; Erie Scientific Company, Portsmouth, NH) placed over the microarray. The whole assembly was sealed in a hybridization chamber (CMT Hybridization Chamber; Corning Incorporated, Corning, NY) and submerged for 16 h in a 46°C water bath. Microarray slides were washed twice for 5 min at 46°C with 1X SSC-0.1% SDS; twice for 10 min at room temperature with 0.1X SSC-0.1% SDS and five times for 1 min at room temperature with 0.1 X SSC. Slides were dried by centrifugation at 50 X g for 3 min and were immediately scanned and analyzed.

scan_protocol: Slides were scanned with an Axon 4000B scanner and GenePix 5.0 used for spot finding. Only spots with more than 80% of pixels greater than background plus 2 standard deviations in either Cy5 or Cy3 channel were used for analysis.

data_processing: Analysis was performed with Limma (Linear models for microarrays data) library in the CARMAweb environment. The background correction was done by background subtraction of the median value, followed by within and between arrays data normalization using the print tip Lowess method, and quantile method, respectively.

organism: Exiguobacterium artemiae 255-15

source_name: E. sibiricum 255-15 grown at -2.5°C labeled with Cy5 (red)

label_protocol: Amino-allyl labeling was performed as adapted from a protocol of The Institute for Genomic Research (TIGR) (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml). Briefly, 10 ug of total RNA was used to synthesize cDNA overnight at 42°C using 0.5 mM of Random Hexamer Primers (Invitrogen, Carlsbad, CA), 3:2 ratio of 5-(3-amino-allyl)-dUTP and dTTP (Ambion), and Superscript II reverse transcriptase (Invitrogen), and subsequently labeled by coupling reactive Cy5 or Cy3 fluorophores (Amersham, Piscataway, NJ) to the amino-allyl groups. Purification after cDNA synthesis and chemical coupling were performed using QiaQuick PCR purification columns (Qiagen) as described in TIGR protocol. The quantity of labeled cDNA and the fluorophore incorporation efficiency were determined by using UV-visible spectrophotometry.

growth_protocol: All the cells for the DNA microarray experiments came from the same E. sibiricum 255-15 frozen stock that was used for the genome sequencing. All experiments were performed by first plating the cells in 1/2 Tryptic Soy Agar  (TSA) and then transferred to 1/2 Tryptic Soy Broth (TSB) twice. In total, six samples were grown independently at 39°C, 28°C, 10°C and -2.5°C. The cells were acclimated by growth at 39°C, 28°C, 10°C and -2.5°C. For the growth at 39°C and 28°C the plates were incubated overnight. At 10°C, the plates were incubated for 3 to 4 days. At -2.5°C the plates were transferred three times to new plates to acclimate the cells to lower temperature as follows: the first plates were incubated overnight at 22°C followed by incubation at 4°C for 3 days and then for 2-3 weeks at -2.5°C.

extract_protocol: The samples were incubated until reaching mid-log growth (0.1 < OD600 < 0.3) when 100 ml of RNAlater (Ambion, Austin, Texas) was added at the same temperature as the grown cells. Cells were pelleted by centrifugation at 5,000 X g for 20 min at 4°C and resuspended in 1 ml of RNAlater, transferred to a 1.5 ml microcentrifuge tube, and re-pelleted at 5,000 X g at 4°C for 10 min.The cells were re-suspended in 100 ul of RNase-free 3 mg ml-1 Lysozyme in TE buffer pH 8 (50 mM Tris-Cl and 1 mM EDTA) by vortexing and then incubated at room temperature for at least 20 min or until the pellet cleared. The RNA was then isolated using the RNeasy mini Prep kit (Qiagen) according to the manufacturer's instructions; the step of DNase digestion was included. The resulting RNA was checked by denaturing agarose gel electrophoresis for DNA contamination and for the presence and integrity of the rRNA bands. The amount of RNA was quantified using a UV-spectrophotometer at OD260.

treatment_protocol: After growing the cells in agar at the four temperatures, a colony from each plate was transferred to tubes containing 5 ml 1/2 TSB and grown in its respective temperatures until an optical density at 600 nm (OD600) of 1.0 was attained. Then 1 ml of this culture was used to inoculate 100 ml of 1/2 TSB in a Nephlo Flask (Belco) for the experiment.

tag: strain 255-15 grown at -2.5°C

source_name: E. sibiricum 255-15 grown at 10°C labeled with Cy3 (green)

tag: strain 255-15 grown at 10°C


title: Comparison -2.5°C versus 10°C - Replicate 2

description: Biological replicate 5 of 6 and dye swap


title: Comparison 10°C versus -2.5°C - Replicate 2

description: Biological replicate 2 of 6

source_name: E. sibiricum 255-15 grown at 10°C labeled with Cy5 (red)

source_name: E. sibiricum 255-15 grown at -2.5°C labeled with Cy3 (green)


title: Comparison 10°C versus -2.5°C - Replicate 3

description: Biological replicate 3 of 6


title: Comparison 10°C versus -2.5°C - Replicate 1

description: Biological replicate 1 of 6


title: Comparison -2.5°C versus 39°C - Replicate 3

source_name: E. sibiricum 255-15 grown at 39°C labeled with Cy3 (green)

tag: strain 255-15 grown at 39°C


title: Comparison -2.5°C versus 39°C - Replicate 2


title: Comparison -2.5°C versus 10°C - Replicate 1

description: Biological replicate 4 of 6 and dye swap


title: Comparison -2.5°C versus 39°C - Replicate 1


title: VAP_patient29_time1


title: Comparison 39°C versus -2.5°C - Replicate 3

description: Biological replicate 3 of 6

source_name: E. sibiricum 255-15 grown at 39°C labeled with Cy5 (red)


title: Comparison 28°C versus -2.5°C - Replicate 2

description: Biological replicate 2 of 6

source_name: E. sibiricum 255-15 grown at 28°C labeled with Cy5 (red)

tag: strain 255-15 grown at 28°C


title: Comparison -2.5°C versus 28°C - Replicate 2

source_name: E. sibiricum 255-15 grown at 28°C labeled with Cy3 (green)


title: Comparison 39°C versus -2.5°C - Replicate 1

description: Biological replicate 1 of 6


title: Comparison -2.5°C versus 28°C - Replicate 1


title: Comparison 28°C versus -2.5°C - Replicate 3

description: Biological replicate 3 of 6


title: Comparison 28°C versus -2.5°C - Replicate 1

description: Biological replicate 1 of 6


title: Comparison 39°C versus 10°C - Replicate 2


title: Comparison 39°C versus 10°C - Replicate 3


title: Comparison 39°C versus 10°C - Replicate 1


title: Comparison 10°C versus 39°C - Replicate 3

description: Biological replicate 3 of 6


title: Comparison 10°C versus 39°C - Replicate 2

description: Biological replicate 2 of 6


title: Comparison 10°C versus 39°C - Replicate 1

description: Biological replicate 1 of 6


title: VAP_patient2_time21

value: Acinetobacter calcoaceticus-baumanii & Serratia marcescens (Gram negative)


title: Comparison 28°C versus 39°C - Replicate 2


title: Comparison 28°C versus 39°C - Replicate 3


title: Comparison -2.5°C versus 28°C - Replicate 3


title: Comparison 28°C versus 39°C - Replicate 1


title: VAP_patient29_time17


title: Comparison 39°C versus 28°C - Replicate 2

description: Biological replicate 2 of 6


title: Comparison 39°C versus 28°C - Replicate 1

description: Biological replicate 1 of 6


title: Comparison 39°C versus 28°C - Replicate 3

description: Biological replicate 3 of 6


title: Comparison 28°C versus 10°C - Replicate 1


title: Comparison 10°C versus 28°C - Replicate 3

description: Biological replicate 3 of 6


title: Comparison 10°C versus 28°C - Replicate 1

description: Biological replicate 1 of 6


title: Comparison 28°C versus 10°C - Replicate 3


title: Comparison 10°C versus 28°C - Replicate 2

description: Biological replicate 2 of 6


title: LHC 611

status: Public on Feb 10 2008

type: genomic

city: Durham

first: Piotr

middle: Andrzej

last: Mieczkowski

state: NC

address: CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 611 strain

hyb_protocol: DNA was hybridized according to Lemoine et al 2005, Cell 120:587.

scan_protocol: Arrays were scanned with a GenePix 4000B scanner. Red and Green PMT gain were manually adjusted to about equal brightness in each channel. Pixel size was 10um and 2 lines were averaged.

data_processing: The data in the VALUE column was obtained by analyzing the data deposited at the University of North Carolina Microarray database (genome.unc.edu). The data from repeated arrays were collapsed to a single value per spot and centered acoording to the median. The VALUE corresponds to the Log2 RED/GREEN Normalized ratio based on the Median.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Reference strain genomic DNA

label_protocol: DNA was labelled according to Lemoine et al 2005, Cell 120:587.

extract_protocol: DNA was prepared according to Lemoine et al 2005, Cell 120:587.

tag: Reference strain genomic DNA

source_name: LHC 611 isolate genomic DNA

tag: LHC 611 isolate genomic DNA


title: LHC 613

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 613 strain

source_name: LHC 613 isolate genomic DNA

tag: LHC 613 isolate genomic DNA


title: LHC 89

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 89 strain

source_name: LHC 89 isolate genomic DNA

tag: LHC 89 isolate genomic DNA


title: LHC 34

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 34 strain

source_name: LHC 34 isolate genomic DNA

tag: LHC 34 isolate genomic DNA


title: Comparison 28°C versus 10°C - Replicate 2


title: LHC 279

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 279 strain

source_name: LHC 279 isolate genomic DNA

tag: LHC 279 isolate genomic DNA


title: LHC 580

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 580 strain

source_name: LHC 580 isolate genomic DNA

tag: LHC 580 isolate genomic DNA


title: LHC 294

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 294 strain

source_name: LHC 294 isolate genomic DNA

tag: LHC 294 isolate genomic DNA


title: LCH 270

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 270 strain

source_name: LHC 270 isolate genomic DNA

tag: LHC 270 isolate genomic DNA


title: LHC 274

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and LHC 274 strain

source_name: LHC 274 isolate genomic DNA

tag: LHC 274 isolate genomic DNA


title: Transcription profiling of Esophageal Tumor Sample_F_755

status: Public on Feb 09 2008

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: The fragmented cRNA were mixed with 55ul of 2x Hybridization Buffer (Agilent). About 110ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done.A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

source_name: Cancer Sample

label_protocol: 825ng of each Cyanine 3 or Cyanine 5 labeled cRNA in a volume of 41.8ul were combined with 11ul of 10x Blocking agent and 2.2ul of 25x Fragmentation buffer (Agilent), and incubated at 60deg C for 30 minutes in dark.

extract_protocol: Trizol

tag: RNA from Oespharyngeal cancer positive patient

source_name: Normal individual

tag: RNA from normal individuals Oesopharynx


title: Transcription profiling of Esophageal Tumor Sample_F_753


title: Transcription profiling of Esophageal Tumor Samples_NF_417


title: Transcription profiling of Esophageal Tumor Sample_F_757


title: Transcription profiling of Esophageal Cancer Sample_NF_053


title: Transcription profiling of Esophageal Tumor Sample_NF_811


title: Transcription profiling of Esophageal Tumor Sample_F_746


title: Transcription profiling of Esophageal Tumor Sample_F_745


title: Transcription profiling of Esophageal Tumor Sample_NF_041


title: Transcription profiling of Esophageal Tumor Sample_F_754


title: Transcription profiling of Esophageal Tumor Sample_F_747


title: Transcription profiling of EsophagealTumor Sample_F_744


title: WT-GFP-lamin A Induction: day 5 Replicate A (2a_WT_5d_A)

city: Bethesda

first: paola

last: scaffidi

state: MD

address: 41 Library Drive, B508

institute: NCI, NIH

description: Labelling, hybridisation and data analysis was performed by GenUs Biosystems

hyb_protocol: cRNA was fragmented to uniform size. CodeLink Bioarrays were hybridized with the cRNA target and stained with Cy5-streptavidin

scan_protocol: Slides were washed and then scanned on an Axon GenePix 4000B scanner

data_processing: Data was analyzed with CodeLink and GeneSpring software packages

label: Biotin

source_name: hTERT-immortalized human skin fibroblasts

label_protocol:
First and second strand cDNA was prepared from the total RNA samples
Biotinylated cRNA target was prepared from the DNA template.

extract_protocol: RNA extracted with Qiagen coulumns

tag: Cell line expressing inducible wt-GFP-lamin A. Induction

value: day 5. Replicate A


title: GFP-progerin Induction: day 10 Replicate B (6b_progerin_10d_B)

tag: Cell line expressing inducible GFP-progerin. Induction

value: day 10. Replicate B


title: GFP-progerin Induction: day 10 Replicate A (6a_progerin_10d_A)

value: day 10. Replicate A


title: WT-GFP-lamin A Induction: day 10 Replicate A (3a_WT_10d_A)


title: GFP-progerin Induction: day 5 Replicate B (5b_progerin_5d_B)

value: day 5. Replicate B


title: GFP-progerin Induction: day 5 Replicate A (5a_progerin_5d_A)


title: WT-GFP-lamin A Induction: day 10 Replicate B (3b_WT_10d_B)


title: GFP-progerin Induction: day 0 Replicate B (4b_progerin_0d_B)

value: day 0. Replicate B


title: GFP-progerin Induction: day 0 Replicate A (4a_progerin_0d_A)

value: day 0. Replicate A


title: 90DAP_high_vs_90DAP_normal

status: Public on Feb 03 2008

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Potato plants of the cultivar 'Atlantic', which is IHN-susceptible, were grown in the greenhouse under a 16-hour photoperiod and 22 C day/18 C night temperatures for 46 days, after which they were transferred to growth chambers with a 14-hour photoperiod and normal (20 C day/18 C night) temperatures.               At 71 DAP (days after planting), half of the plants were subjected to high (28 C day/20 C night) temperatures for the remainder of the study.  Tubers from both normal and high temperature regimes were harvested at two-week intervals, beginning at 76 DAP and ending at 118 DAP.  For each RNA sample, equal amounts of peeled tuber tissue (sampled from the center of the tuber using a cork borer) was pooled from three randomly chosen plants.  RNA was extracted using a hot-phenol and high salt (2.4 M) CTAB-based extraction buffer.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Grown in growth chamber with 14-hour photoperiod, gravel-peat-vermiculite substrate

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: Grown at high temperature (28 C day/18 C night), harvested 90 days after planting

tag: Solanum tuberosum, Peeled tuber, Abiotic stress

treatment_protocol: Grown at normal temperature (20 C day/18 C night), harvested 90 days after planting


title: WT-GFP-lamin A Induction: day 5 Replicate B (2b_WT_5d_B)


title: 104DAP_normal_vs_90DAP_high

treatment_protocol: Grown at normal temperature (20 C day/18 C night), harvested 104 days after planting


title: 90DAP_normal_vs_104DAP_high

treatment_protocol: Grown at high temperature (28 C day/18 C night), harvested 104 days after planting


title: WT-GFP-lamin A Induction: Day 0 Replicate A (CBGE_Hsapiens_WG_progerin1)

source_name: hTERT-immortalized skin fibroblast cell line

tag: cell line expressing inducible wt-GFP-lamin A. Induction

value: Day 0. Replicate A


title: WT-GFP-lamin A Induction: day 0 Replicate B (1b_WT_0d_B)


title: 104DAP_high_vs_104DAP_normal


title: 118DAP_high_vs_76DAP_high

treatment_protocol: Grown at high temperature (28 C day/18 C night), harvested 118 days after planting

treatment_protocol: Grown at high temperature (28 C day/18 C night), harvested 76 days after planting


title: 76DAP_high_vs_76DAP_normal

treatment_protocol: Grown at normal temperature (20 C day/18 C night), harvested 76 days after planting


title: 118DAP_normal_vs_118DAP_high

treatment_protocol: Grown at normal temperature (20 C day/18 C night), harvested 118 days after planting


title: VAP_patient18_time11

description: Gene expression data (Affy Chip Hg-Focus)

tag: Tissue

tag: VAP

tag: Gender

value: Female

tag: Age

tag: Ethnicity

tag: Infecting Organism


title: 118DAP_normal_vs_76DAP_high


title: 76DAP_normal_vs_118DAP_normal


title: 76DAP_normal_vs_90DAP_normal


title: HL60_+IM_3h

status: Public on Feb 01 2008

city: Lund

first: Petra

last: Johnels

address: Lund University Hospital

department: Clinical Genetics

country: Sweden

institute: Lund University

description: cDNA microarray data

hyb_protocol: Arrays were hybridized and washed as described in Håkansson et al. (Genes Chromosomes Cancer 2008)

scan_protocol: Arrays were scanned in an Agilent Microarray scanner

data_processing: Image analysis was performed using Gene Pix v4.0. Result-files were uploaded into BASE where they were normalized using pin-based Lowess and filtered to keep spots with a signal to noise ratio >1.5

label_protocol: Samples were labeled using the CyScribe Post-labeling Kit (Amersham Biosciences)

extract_protocol: Trizol extraction followed by purification using RNeasy

treatment_protocol: imatinib mesylate

tag: Ph- cell line

source_name: Stratagene Universal Human Reference RNA

tag: RNA pooled from ten human cell lines


title: 76DAP_high_vs_90DAP_high


title: HL60_+IM_12h

description: cDNA microarray data


title: 697_untreated_12h

description: cDNA microarray data


title: 697_+IM_3h

description: cDNA microarray data


title: HL60_untreated_3h

description: cDNA microarray data


title: 697_untreated_3h

description: cDNA microarray data


title: 104DAP_high_vs_118DAP_high


title: 90DAP_high_vs_104DAP_high


title: RS4;11_+IM_12h_technical replicate 2

description: cDNA microarray data


title: HL60_untreated_12h

description: cDNA microarray data


title: 104DAP_normal_vs_118DAP_normal


title: RS4;11_+IM_3h_technical replicate 2

description: cDNA microarray data


title: RS4;11_untreated_3h_technical replicate 2

description: cDNA microarray data


title: RS4;11_untreated_12h_technical replicate 2

description: cDNA microarray data


title: 90DAP_normal_vs_104DAP_normal


title: 697_+IM_12h

description: cDNA microarray data


title: 118DAP_high_vs_76DAP_normal


title: RS4;11_+IM_12h_technical replicate 1

description: cDNA microarray data


title: DC +ICAM3 vs. DC control

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Human peripheral blood mononuclear cells (PBMCs) were isolated from blood obtained from voluntary donors. Patients gave informed consent and all studies were conducted in accordance with local ethics committees. Buffy coats were recovered from interphase of ficoll gradients according to standard protocols. To obtain untouched monocytes, cells were subjected to negative MACS selection using MonoMACS II Isolation Kit (Miltenyi). Flowthrough cells were collected and grown in complete RPMI1640 medium containing 200 U/ ml hGM-CSF and 200 U/ ml hIL-4 (Strathmann) for 7 days to obtain immature, untouched DCs. For stimulation experiments, cells were grown in 10 ml medium in 6-well plates

hyb_protocol: Agilent GE Hyb Kit (5188-5242) according supplier's protocol

scan_protocol: Agilent Scanner BA, 5µm resolution according supplier's protocol

data_processing: Features were extracted with an image analysis tool version A.6.1.1 (Agilent Technologies) using default settings. Data analysis was carried out on the Rosetta Inpharmics platform Resolver Version 5.0. Ratio profiles were combined in an error-weighted fashion with Resolver to create ratio experiments. A 1.5 fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value > 0.05), robust and reproducible.

source_name: DC +ICAM3

label_protocol: Agilent low RNA Input Linear Amp Kit two-color (5188-5340)

extract_protocol: Total RNA was isolated by the TRIzol® Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) according the supplier's protocol

tag: DCs were stimulated with recombinant ICAM3 at a concentration of 15 Âµg/ml for 18 h. ICAM-3-Fc-Chimera was obtained from R&D Systems. The Fc part was cut off by digestion with Factor Xa (Novagen) and removed by incubation with ProteinA sepharose (Amersham). For aggregate formation, ICAM-3 solution was highly concentrated on Centricon filter units (Millipore). Purity of ICAM-3 and absence of Fc fragments were confirmed by SDS-PAGE and immunoblot.

source_name: DC control

tag: DC were kept unstimulated


title: RS4;11_+IM_3h_technical replicate 1

description: cDNA microarray data


title: DC control vs. DC +ICAM3

tag: DCs were stimulated with recombinant ICAM3 at a concentration of 15 µg/ml for 18 h. ICAM-3-Fc-Chimera was obtained from R&D Systems. The Fc part was cut off by digestion with Factor Xa (Novagen) and removed by incubation with ProteinA sepharose (Amersham). For aggregate formation, ICAM-3 solution was highly concentrated on Centricon filter units (Millipore). Purity of ICAM-3 and absence of Fc fragments were confirmed by SDS-PAGE and immunoblot.


title: RS4;11_untreated_12h_technical replicate 1

description: cDNA microarray data


title: RS4;11_untreated_3h_technical replicate 1

description: cDNA microarray data


title: MonoMac6_untreated_3h_technical replicate 2

description: cDNA microarray data


title: Comparison 39°C versus -2.5°C - Replicate 2

description: Biological replicate 2 of 6

source_name: E. sibiricum 255-15 grown at 39°C labeled with Cy5 (red)

tag: strain 255-15 grown at 39°C

source_name: E. sibiricum 255-15 grown at -2.5°C labeled with Cy3 (green)

tag: strain 255-15 grown at -2.5°C


title: MonoMac6_untreated_12h_technical replicate 2

description: cDNA microarray data


title: MonoMac6_+IM_12h_technical replicate 2

description: cDNA microarray data


title: DC control vs. DC +ManLAM

source_name: DC +ManLAM

tag: DCs were stimulated with mycobacterial ManLAM at a concentration of 15 Âµg/ml for 18 h.


title: MonoMac6_untreated_12h_technical replicate 1

description: cDNA microarray data


title: MonoMac6_+IM_3h_technical replicate 1

description: cDNA microarray data


title: MonoMac6_+IM_12h_technical replicate 1

description: cDNA microarray data


title: U937_+IM_12h_technical replicate 2

description: cDNA microarray data


title: MonoMac6_+IM_3h_technical replicate 2

description: cDNA microarray data


title: U937_untreated_3h_technical replicate 2

description: cDNA microarray data


title: U937_+IM_3h_technical replicate 2

description: cDNA microarray data


title: U937_untreated_12h_technical replicate 2

description: cDNA microarray data


title: Transcription profiling of Esophageal Tumor Sample_NF_047

tag: RNA from Oespharyngeal cancer positive patient

tag: RNA from normal individuals Oesopharynx


title: DC control vs. DC +ManLAM exp1


title: DC +ManLAM vs. DC control exp1


title: U937_untreated_12h_technical replicate 1

description: cDNA microarray data


title: MonoMac6_untreated_3h_technical replicate 1

description: cDNA microarray data


title: DC +ManLAM vs. DC control

tag: DCs were stimulated with mycobacterial ManLAM at a concentration of 15 µg/ml for 18 h.

source_name: unstimulated DC


title: U937_+IM_3h_technical replicate 1

description: cDNA microarray data


title: U937_untreated_3h_technical replicate 1

description: cDNA microarray data


title: U937_+IM_12h_technical replicate 1

description: cDNA microarray data


title: Meg01_+IM_3h_technical replicate 2

description: cDNA microarray data

tag: Ph+ cell line


title: Meg01_+IM_12h_technical replicate 2

description: cDNA microarray data


title: Meg01_untreated_12h_technical replicate 2

description: cDNA microarray data


title: Meg01_untreated_3h_technical replicate 2

description: cDNA microarray data


title: LAMA84_+IM_3h_technical replicate 2

description: cDNA microarray data


title: LAMA84_+IM_3h_technical replicate 1

description: cDNA microarray data


title: LAMA84_untreated_3h_technical replicate 2

description: cDNA microarray data


title: LAMA84_+IM_12h_technical replicate 2

description: cDNA microarray data


title: LAMA84_untreated_12h_technical replicate 2

description: cDNA microarray data


title: Meg01_+IM_12h_technical replicate 1

description: cDNA microarray data


title: LAMA84_+IM_12h_technical replicate 1

description: cDNA microarray data


title: Meg01_+IM_3h_technical replicate 1

description: cDNA microarray data


title: Meg01_untreated_3h_technical replicate 1

description: cDNA microarray data


title: Meg01_untreated_12h_technical replicate 1

description: cDNA microarray data


title: JK1_untreated_3h_technical replicate 2

description: cDNA microarray data


title: JK1_untreated_12h_technical replicate 2

description: cDNA microarray data


title: JK1_untreated_12h_technical replicate 1

description: cDNA microarray data


title: JK1_untreated_3h_technical replicate 1

description: cDNA microarray data


title: JK1_+IM_12h_technical replicate 2

description: cDNA microarray data


title: JK1_+IM_3h_technical replicate 2

description: cDNA microarray data


title: LAMA84_untreated_3h_technical replicate 1

description: cDNA microarray data


title: LAMA84_untreated_12h_technical replicate 1

description: cDNA microarray data


title: KU812_+IM_12h_technical replicate 1

description: cDNA microarray data


title: KU812_untreated_3h_technical replicate 2

description: cDNA microarray data


title: KU812_+IM_12h_technical replicate 2

description: cDNA microarray data


title: KU812_untreated_12h_technical replicate 2

description: cDNA microarray data


title: JK1_+IM_3h_technical replicate 1

description: cDNA microarray data


title: KU812_+IM_3h_technical replicate 1

description: cDNA microarray data


title: KU812_+IM_3h_technical replicate 2

description: cDNA microarray data


title: JK1_+IM_12h_technical replicate 1

description: cDNA microarray data


title: KU812_untreated_3h_technical replicate 1

description: cDNA microarray data


title: K562_untreated_12h_technical replicate 2

description: cDNA microarray data


title: KU812_untreated_12h_technical replicate 1

description: cDNA microarray data


title: K562_+IM_3h_technical replicate 2

description: cDNA microarray data


title: K562_+IM_12h_technical replicate 2

description: cDNA microarray data


title: K562_+IM_3h_technical replicate 1

description: cDNA microarray data


title: K562_untreated_3h_technical replicate 2

description: cDNA microarray data


title: K562_+IM_12h_technical replicate 1

description: cDNA microarray data


title: K562_untreated_3h_technical replicate 1

description: cDNA microarray data


title: Yeast aging 8 generation microarray 4

city: Claremont

first: Laura

middle: L. Mays

last: Hoopes

state: CA

address: 175 6th Street

department: Biology

institute: Pomona College

description:
Yeast aging 8 generation microarray 4
see paper, J Gerontol Jan, 2008

hyb_protocol: amplified labeled RNA was denatured and hybridized with Genome Consortium for Active Teaching (GCAT) yeast microarray overnight at 37 degrees C in denaturing buffer (see J Gerontol Jan, 2008 for details).

scan_protocol: Axon GenePix 4000B scanner with GenePix 5.1 software.

data_processing: Data filtered and normalized (loess) in Bioconductor software.  Statistical analyses were run in that software to determine genes significantly changed in expression with aging.

source_name: 8 generation old yeast

label_protocol: cDNA was made with incorporation of T7 promoter; RNA was amplified including amino allyl derivative; aRNA was coupled with activated dye.  See paper, J Gerontol Jan 2008 for details.

growth_protocol: see paper, J Gerontol, Jan, 2008.  Note that cells were magnetically sorted with Miltenyi beads and never allowed to go above .8 A600, so they were maintained in log phase.

extract_protocol: see paper, J Gerontol, Jan, 2008.  Basically glass bead grinding and RNEasy column preparation, followed by quality control tests.

treatment_protocol: see paper, J Gerontol, Jan, 2008

tag: Yeast RNA amplified from 8 generation old cells

source_name: 1 generation old yeast

tag: Yeast RNA amplified from sample of 1 generation cells treated in parallel with the sample in Channel 1 to avoid differential gene expression for stress response genes


description:
Yeast Aging 18-20 generation microarray 4 (dye inversion)
see paper, J Gerontol Jan, 2008

source_name: 18-20 generation old yeast

tag: Yeast RNA amplified from 18-20 generation old cells


title: K562_untreated_12h_technical replicate 1

description: cDNA microarray data


title: Yeast aging 12 generation microarray 2

description:
Yeast aging 12 generation microarray 2
see paper, J Gerontol Jan, 2008

source_name: 12 generation old yeast

tag: Yeast RNA amplified from 12 generation old cells


description:
Yeast aging 8 generation microarray 1 (dye inversion)
see paper, J Gerontol Jan, 2008


description:
Yeast aging 8 generation microarray 6 (dye inversion)
see paper, J Gerontol Jan, 2008


title: Yeast aging 8 generation microarray 5

description:
Yeast aging 8 generation microarray 5
see paper, J Gerontol Jan, 2008


description:
Yeast aging 18-20 generation microarray 6 (dye inversion)
see paper, J Gerontol Jan, 2008


description:
Yeast aging 18-20 generation microarray 3
see paper, J Gerontol Jan, 2008


description:
Yeast aging 18-20 generation microarray 5
see paper, J Gerontol Jan, 2008


title: Yeast aging 1 generation microarray 7

description:
Yeast aging 1 generation microarray 7
see paper, J Gerontol Jan, 2008

tag: Yeast RNA amplified from 1 generation old cells


description:
Yeast aging 8 generation microarray 2 (dye inversion)
see paper, J Gerontol Jan, 2008


description:
Yeast aging 18-20 generation microarray 1
see paper, J Gerontol Jan, 2008


title: Yeast aging 12 generation microarray 6

description:
Yeast aging 12 generation microarray 6
see paper, J Gerontol Jan, 2008


description:
Yeast aging 12 generation microarray 5 (dye inversion)
see paper, J Gerontol Jan, 2008


description:
Yeast aging 18-20 generation microarray 2 (dye inversion)
see paper, J Gerontol Jan, 2008


description:
Yeast aging 12 generation microarray 7 (dye inversion)
see paper, J Gerontol Jan, 2008


title: Yeast aging 1 generation microarray 1

description:
Yeast aging 1 generation microarray 1
see paper, J Gerontol Jan, 2008


description:
Yeast aging 18-20 generation microarray 7
see paper, J Gerontol Jan, 2008


description:
Yeast aging 12 generation microarray 3 (dye inversion)
see paper, J Gerontol Jan, 2008


title: Yeast aging 1 generation microarray 3

description:
Yeast aging 1 generation microarray 3
see paper, J Gerontol Jan, 2008


title: yeast aging 12 generation microarray 4

description:
yeast aging 12 generation microarray 4
see paper, J Gerontol Jan, 2008


description:
Yeast aging 1 generation microarray 2 (dye inversion)
see paper, J Gerontol Jan, 2008


title: Dehalococcoides ethenogenes_Transition Phase_Replicate 2

city: Dübendorf

first: David

middle: R

last: Johnson

address: Uberlandstrasse 133

department: Environmental Microbiology

country: Switzerland

institute: Eawag

description: Not available

hyb_protocol: The hybridization protocol is described in detail in Section 3 of the Affymetrix GeneChip Expression Analysis Technical Manual available on-line (www.affymetrix.com).

scan_protocol: The scan protocol is described in detail in Section 3 of the Affymetrix GeneChip Expression Analysis Technical Manual available on-line (www.affymetrix.com). An Affymetrix Scan3000 scanner was used.

data_processing: Data was processed using MAS5.0 with global scaling to a value of 2500.

organism: Dehalococcoides mccartyi 195

source_name: Dehalococcoides ethenogenes 195 in the transition growth-phase

label_protocol: The label protocol is described in detail in Section 3 of the Affymetrix GeneChip Expression Analysis Technical Manual available on-line (www.affymetrix.com).

growth_protocol: Cells were grown with completely defined medium with trichloroethene as the electron acceptor, acetate as the carbon source, and hydrogen as the electron donor. A detailed description of the growth protocol is described in the following: He et al. 2007. Appl. Environ. Microbiol. 73(9) 2847-2853.

extract_protocol: Cells were collected by filtration through 0.2 um pore size Durapore hydrophilic membrane filters from 100 ml cultures. RNA was extracted using a standard acid-phenol technique described in detail in the following: Johnson et al. 2005. Appl. Environ. Microbiol. 71(7) 3866-3871.

treatment_protocol: Cells were grown with trichloroethene to the transition phase

tag: Organism

value: Dehalococcoides ethenogenes; Strain:195; Growth phase:transition


title: Dehalococcoides ethenogenes_Late Stationary Phase_Replicate 1

description: Not available

source_name: Dehalococcoides ethenogenes 195 in the late stationary growth-phase

treatment_protocol: Cells were grown with trichloroethene to the late stationary phase

value: Dehalococcoides ethenogenes; Strain:195; Growth phase:late stationary


title: Dehalococcoides ethenogenes_Late Stationary Phase_Replicate 3

description: Not available


title: Yeast aging 8 generation microarray 3 (dye inversion)

description:
Yeast aging 8 generation microarray 3
see paper, J Gerontol Jan, 2008


title: Dehalococcoides ethenogenes_Late Stationary Phase_Replicate 2

description: Not available


title: Dehalococcoides ethenogenes_Transition Phase_Replicate 3

description: Not available


title: Dehalococcoides ethenogenes_Late Exponential Phase_Replicate 2

description: Not available

source_name: Dehalococcoides ethenogenes 195 in the late exponential growth-phase

treatment_protocol: Cells were grown with trichloroethene to the late exponential phase

value: Dehalococcoides ethenogenes; Strain:195; Growth phase:late exponential


title: Dehalococcoides ethenogenes_Early Exponential Phase_Replicate 3

description: Not available

source_name: Dehalococcoides ethenogenes 195 in the early exponential growth-phase

treatment_protocol: Cells were grown with trichloroethene to the early exponential phase

value: Dehalococcoides ethenogenes; Strain:195; Growth phase:early exponential


title: Dehalococcoides ethenogenes_Late Exponential Phase_Replicate 3

description: Not available


title: Yeast aging 1 generation microarray 5

description:
Yeast aging 1 generation microarray 5
see paper, J Gerontol Jan, 2008


title: Dehalococcoides ethenogenes_Transition Phase_Replicate 1

description: Not available


title: Yeast aging 1 generation microarray 6

description:
Yeast aging 1 generation microarray 6
see paper, J Gerontol Jan, 2008


title: Dehalococcoides ethenogenes_Late Exponential Phase_Replicate 1

description: Not available


title: Dehalococcoides ethenogenes_Early Stationary Phase_Replicate 1

description: Not available

source_name: Dehalococcoides ethenogenes 195 in the early stationary growth-phase

treatment_protocol: Cells were grown with trichloroethene to the early stationary phase

value: Dehalococcoides ethenogenes; Strain:195; Growth phase:early stationary


title: Dehalococcoides ethenogenes_Early Exponential Phase_Replicate 1

description: Not available


title: Dehalococcoides ethenogenes_Early Stationary Phase_Replicate 3

description: Not available


title: Peritoneal Carcinomatosis of gastric cancer 3+ versus 1-

status: Public on Jan 31 2008

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: Slides were scanned in a microarray scanner (Genetix Limited, Hampshire, UK). Photomultiplier tube voltage was set to 100% for both red and green channels. The two resulting green and red images were overlaid using ImaGene 5 (BioDiscovery, Inc., CA, USA).

hyb_protocol: Pre-hybridization Note: Do not allow the slides to dry during the pre-hybridization and washing procedure. 1. Pre-warm an appropriate volume of Nexterion 70mer Oligo Pre-Hyb to 48°C for 10 minutes until the precipitate is completely dissolved. 2. Incubate slides in Nexterion 70mer Oligo Pre-Hyb for 45 min at 48°C. Use a large enough volume of buffer to ensure that all slides are completely covered with Nexterion Pre-Hyb. 3. During the pre-hybridization step, prepare Wash Solution 1 by diluting Nexterion 70mer Oligo Wash B 1:40 with diH2O. Prepare 50 ml per slide (i.e. 1.25 ml Nexterion 70mer Oligo Wash B, add diH2O to 50 ml). 4. Wash 5 min in Wash Solution 1 at 20 to 25°C. 5. Rinse with diH2O for 30 sec. 6. Dry the Nexterion Slide E with nitrogen. Hybridization Prewarm Hybsolution 15 minutes before hybridization at 68°C. Clean coverslips with dH20 and 100% Ethanol and dry the coverslips with nitrogen. 1. Pipette 40µl of hybridization to the solution. Denature the fragmented target in the hyb-buffer by heating at 95°C for 3 min. Then let the probe cool down for 1 min at RT. Afterwards place the target onto the array surface of a prehybridized slide under the coverslip 3. Hybridize the slide at 48°C for 16 hours. Post-hybridization washing Note: Do not allow the slides to dry during the hybridization and washing procedure. Wash Solution 2, 3 and 4 should be prepared in advance. Use at least 50 ml solution per slide. Post-hybridization washing solutions: Preparation: Wash Solution 2: 50 ml Nexterion 70mer Oligo Wash A, 25 ml Nexterion 70mer Oligo Wash B, Make up to 500 ml with diH2O Wash Solution 3: 50 ml Nexterion 70mer Oligo Wash A, Make up to 500 ml with diH2O Wash Solution 4: 5 ml Nexterion 70mer Oligo Wash A, Make up to 500 ml with diH2O 1. Place the array into a slide rack and immerse in a dish containing Wash Solution 2. Wash in the above solution 1 x 10 min at 20 to 25°C. 2. Wash 1 x 10 min in Wash Solution 3 at 20 to 25°C. 3. Wash 1 x 10 min in Wash Solution 4 at 20 to 25°C. 4. Dry the array with nitrogen. 5. Protect the array from light, dust and abrasion of the array surface, until ready for scanning.

scan_protocol: not further discription needed

data_processing: The data was normalized using loess normalization on the normexp-background corrected expression values, followed by a dye-swap normalization and in-between-array quantile normalization. Both the loess and quantile normalization methods were used as provided in the limma package

molecule: polyA RNA

source_name: Patient No 3 gastric cancer with PC

label_protocol: Amino Allyl MessageAmp II aRNA Amplification Kit performed according to the provided manual

extract_protocol: Machery & Nagel RNA extraction kit performed according to the provided manual

tag: gastric cancer with PC

source_name: Patient No 1 gastric cancer without PC

tag: gastric cancer without PC


title: Dehalococcoides ethenogenes_Early Stationary Phase_Replicate 2

description: Not available


title: Peritoneal Carcinomatosis of gastric cancer 1- versus 2+

source_name: Patient No 1 castric cancer without PC

tag: castric cancer without PC

source_name: Patient No 2 gastric cancer with PC


title: Dehalococcoides ethenogenes_Early Exponential Phase_Replicate 2

description: Not available

growth_protocol:
Cells were grown with completely defined medium with trichloroethene as the electron acceptor, acetate as the carbon source, and hydrogen as the electron donor. A detailed description of the growth protocol is described in the following:
He et al. 2007. Appl. Environ. Microbiol. 73(9) 2847-2853.

extract_protocol:
Cells were collected by filtration through 0.2 um pore size Durapore hydrophilic membrane filters from 100 ml cultures. RNA was extracted using a standard acid-phenol technique described in detail in the following:
Johnson et al. 2005. Appl. Environ. Microbiol. 71(7) 3866-3871.


title: Peritoneal Carcinomatosis of gastric cancer 2+ versus 3-

source_name: Patient No 3 gastric cancer without PC


title: Peritoneal Carcinomatosis of gastric cancer 2- versus 3+

description: no further discription needed

scan_protocol: Slides were scanned in a microarray scanner (Genetix Limited, Hampshire, UK). Photomultiplier tube voltage was set to 100% for both red and green channels. The two resulting green and red images were overlaid using ImaGene 5 (BioDiscovery, Inc., CA, USA).

source_name: Patient No 2 gastric cancer without PC


title: Peritoneal Carcinomatosis of gastric cancer 3- versus 3+


title: Peritoneal Carcinomatosis of gastric cancer 1+ versus 3-

source_name: Patient No 1 gastric cancer with PC


title: Peritoneal Carcinomatosis of gastric cancer 1- versus 1+

source_name: Patient No 1 castric cancer with PC

tag: castric cancer with PC


title: Peritoneal Carcinomatosis of gastric cancer 2- versus 2+


title: MRL liver DCAC3 6wks

city: Galveston

first: Rolf

last: Konig

state: TX

address: 301 University Blvd.

department: Microbiology & Immunology

institute: UTMB

description: This sample is one of three samples from mice treated with dichloroacetyl chloride in an experiment designed to measure the effects of exposure to dichloroacetyl chloride or dichloroacetic anhydride on liver gene expression in female MRL +/+ mice.

hyb_protocol: The biotin-labeled antisense cRNA was fragmented to a mean size of 200 bases, and the biotinylated cRNA-fragments served as targets for microarray hybridization. Standard protocols and a GeneChip Hybridization Oven 640 (Affymatrix) were used. Microarrays were washed in a GeneChip Fluidics Station 400 (Affymetrix) using standard and automated protocols. The washing protocol involves exposure to Phycoerythrin-labeled Streptavidin.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 (Affymetrix) with GeneChip Operating Software.

data_processing: Data were analyzed using GCOS.

label: Phycoerythrin

organism: Mus musculus

source_name: Liver from 11-week-old female MRL +/+ treated for six weeks with dichloroacetyl chloride

label_protocol: Reverse transcription was performed using 10-25 microg of total RNA and an oligo-dT primer that encodes a T7 RNA polymerase promoter sequence for first-strand cDNA synthesis. Second-strand synthesis converted the cDNA into double-stranded DNA templates for use in an in vitro transcription reaction. Bacteriophage T7 RNA polymerase and biotinylated nucleotides were used to produce biotinylated cRNA.

extract_protocol: Total RNA was isolated using the ToTALLY RNA kit from Ambion (Austin, TX) and processed through CHROMA SPIN-100 columns (BD Biosciences Clonetech, Mountain View, CA).

treatment_protocol: Five-week-old mice were injected intraperitoneally with 0.2 mmol/kg of dichloroacetyl chloride in 100 microliter of corn oil twice weekly for six weeks.

tag: Strain

value: MRL +/+; Gender:female; Age:11 weeks; Tissue:liver; Experiment:treatment with dichloroacetyl chloride


title: MRL liver DCAC2 6wks


title: MRL liver DCAA1 6wks

description: This sample is one of three samples from mice treated with dichloroacetic anhydride in an experiment designed to measure the effects of exposure to dichloroacetyl chloride or dichloroacetic anhydride on liver gene expression in female MRL +/+ mice.

source_name: Liver from 11-week-old female MRL +/+ treated for six weeks with dichloroacetic anhydride

treatment_protocol: Five-week-old mice were injected intraperitoneally with 0.2 mmol/kg of dichloroacetic anhydride in 100 microliter of corn oil twice weekly for six weeks.

value: MRL +/+; Gender:female; Age:11 weeks; Tissue:liver; Experiment:treatment with dichloroacetic anhydride


title: Yeast aging 1 generation microarray 4

description:
Yeast aging 1 generation microarray 4
see paper, J Gerontol Jan, 2008

source_name: 1 generation old yeast


title: delta_ccpA_early_rep4

status: Public on Jan 30 2008

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

description: Care was taken during sample processing to ensure equivalent amounts of cDNA were hybridized to each chip.

hyb_protocol: Standard Affymetrix for low G+C bacteria.

scan_protocol: Standard Affymetrix.

data_processing: Values were generated using GCOS.

organism: Streptococcus sp. 'group A'

source_name: delta_ccpA, early growth phase in THY media

label_protocol: Standard Affymetrix Protocol via Affymetrix labeling kit.

growth_protocol: Growth in standard laboratory media (THY) at 37 degrees with 5% CO2

extract_protocol: RNA protect was added at 2:1 volume.  Cells were harvested via centrifugation and snap frozen.  Pellets were resuspended and nucleic acid harvested using phenol-chloroform extraction.  RNA was isolated using Qiagen RNeasy mini-kits.

tag: delta_ccpA is an isogenic mutant strain of MGAS5005


title: delta_ccpA_early_rep2


title: delta_ccpA_rep3


title: MGAS5005_late_rep2

source_name: MGAS5005, late growth phase in THY media

tag: Strain MGAS5005 is an invasive serotype M1 strain


title: MGAS5005_late_rep3


title: Peritoneal Carcinomatosis of gastric cancer 1+ versus 2-

description: not further discription needed


title: MGAS5005_late_rep1


title: MRL liver DCAA3 6wks


title: delta_ccpA_late_rep2

source_name: delta_ccpA, late growth phase in THY media


title: delta_ccpA_early_rep1


title: MRL liver DCAA2 6wks


title: MGAS5005_early_rep3

source_name: MGAS5005, early growth phase in THY media


title: MGAS5005_early_rep4


title: A4-LLOYD-CON_REP1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
location: Growth cabinet
Atmosphere: Normal
Humidity: 60%
Temperature: 23oC
Lighting: 16h light/8h dark
Medium: 1/2 Murashige and Skoog medium (10d) followed by compost
Nutrients: 1% sucrose in Murashige and Skoog medium
Water: Twice a week
Stratification: 3d at 4oC

hyb_protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit according to guidelines set out by Affymetrix, Santa Clara, CA.

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

organism: Arabidopsis thaliana

label_protocol: RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3') was hybridized with the Total RNA ( 8 - 12ug) at 70oC for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour. The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis. 130ul of the second strand reaction mix was added to the 20ul first strand synthesis reaction. The second strand reaction mix contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM beta-NAD+. The reaction was incubated at 16 C for 2 hours. 10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA. The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module. The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix. The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters. The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module. The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA. The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments. 15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.

extract_protocol: Qiagen / Trizol: Qiagen RNAeasy kit protocol

tag: Stock Code

tag: Developmental stage

tag: Tissue

value: Rosette leaves


title: MGAS5005_early_rep1


title: MRL liver DCAC1 6wks


title: MGAS5005_early_rep2


title: Ward_A2-WARD-ax1_SLD

institute: Nottingham Arabidopsis Stock Centre (NASC)

description:
location: Growth Room
Humidity: approx. 60% (normal)
Temperature: 21 C
Lighting: 16 hour light, 8 hour dark
Medium: compost
Treatment: Intercept WG treated soil before sowing
Water: tap water as required
Stratification: 3 days cold treatment on soil

extract_protocol: Qiagen RNEasy columns: As in manufacturers instructions including DNase treatment

value: axillary buds approx. 2 mm elongated

tag: Genetic background

tag: Genetic variation

value: EMS


title: MRL liver control3 11wks

description: This sample served as a control in an experiment designed to measure the effects of exposure to dichloroacetyl chloride or dichloroacetic anhydride on liver gene expression in female MRL +/+ mice.

source_name: Liver from 11-week-old female MRL +/+ control

value: MRL +/+; Gender:female; Age:11 weeks; Tissue:liver; Experiment:untreated


title: MRL liver control1 11wks


title: MRL liver control2 11wks


title: Control IgG for 4 days replicate 1

status: Public on Jan 29 2008

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Chip ID=ingrid-170-U34A-010903.  RNA from P18 day old rat testis.

hyb_protocol: standard Affymetrix protocol

scan_protocol: chips were scanned using Agilent GeneArray Scanner G2500A

data_processing: Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using a scaling factor of 125, and then imported into the GeneSpring program (Agilent Technologies, Palo Alto, CA).

organism: Rattus norvegicus

source_name: Testis from Sprague Dawley male rat 170, Day 18 postnatal, control antibody for 4 days

label_protocol: standard Affymetrix protocol

extract_protocol: About 20 ovaries with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).  Two independent RNA samples were analysed for each treatment group.

treatment_protocol: Male day P18 rat were injected with control IgG for 4 days. Day P22 rat were euthanized and testis were removed according to IACUC-approved animal use protocols.

tag: male rat 170

tag: Testis dissected from P18-day old Sprague Dawley rats

tag: control antibody for 4 days


title: 685_array

city: Foster City

first: Catalin

last: Barbacioru

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description: Gene expression data from peripheral blood of TAA/normal individuals using Applied Biosystems AB1700 Whole Genome Microarray

hyb_protocol: Hybridization was performed according to Applied Biosystems Chemiluminescence Detection Kit Protocol (PN 4339627) using 10 ug fragmented cRNA

scan_protocol: Image was captured using CCD camera came with AB1700 Microarray Analyzer

data_processing: Quantile normalization of training samples using ABarray bioconductor package. Testing samples are quantile normalized to the profile of training samples.

label: digoxigenin

source_name: Peripheral blood

label_protocol: Digoxigenin labeled cRNA was prepared according to Applied Biosystems nanoamp RT-IVT protocol

extract_protocol: PAXgene tube and Qiagen Preanalytics Blood RNA kit

tag: Control; testing set


title: Control IgG for 4 days replicate 2

description: Chip ID=ingrid-172-U34A-010903.  RNA from P18 day old rat testis.

source_name: Testis from Sprague Dawley male rat 172, Day 18 postnatal, control antibody for 4 days

tag: male rat 172


title: 638_array

tag: TAA; testing set


title: 668_array


title: 660_array


title: 658_array


title: 664_array


title: 677_array


title: 661_array


title: Yeast aging 12 generation microarray 1

description:
Yeast aging 12 generation microarray 1
see paper, J Gerontol Jan, 2008

source_name: 12 generation old yeast

tag: Yeast RNA amplified from 12 generation old cells

tag: Yeast RNA amplified from sample of 1 generation cells treated in parallel with the sample in Channel 1 to avoid differential gene expression for stress response genes


title: delta_ccpA_late_rep1


title: 678_array


title: MGAS5005_late_rep4


title: 676_array


title: FSH antibody for 4 days replicate 1

description: Chip ID=ingrid-161-U34A-010903.  RNA from P18 day old rat testis.

source_name: Testis from Sprague Dawley male rat 161, Day 18 postnatal, FSH antibody for 4 days

treatment_protocol: Male day P18 rat were injected with anti-FSH for 4 days. Day P22 rat were euthanized and testis were removed according to IACUC-approved animal use protocols.

tag: male rat 161

tag: FSH antibody for 4 days


title: delta_ccpA_late_rep3

tag: delta_ccpA is an isogenic mutant strain of MGAS5005


title: delta_ccpA_late_rep4


title: 522_array


title: 499_array


title: 675_array


title: 400_array


title: 351_array


title: 330a_array


title: Postnatal day 4 replicate 2

description: Chip ID=ingrid-167-U34A-010903.  RNA from P18 day old rat testis.

source_name: Testis from Sprague Dawley male rat 167 Day 18 postnatal, FSH antibody for 4 days

tag: male rat 167


title: 652_array


title: 399_array


title: 294_array


title: 284_array


title: 683_array


title: 657_array


title: 656_array

tag: testing set


title: 327_array


title: 282_array


title: 330b_array


title: 264_array


title: 278b_array


title: 279_array


title: 278a_array


title: 265_array


title: 565_array

tag: Control; training set


title: 674_array


title: 679_array


title: 563_array


title: 544_array


title: 543_array


title: 541_array


title: 564_array


title: 545_array


title: 269_array


title: 476_array


title: 548_array


title: 542_array


title: 547_array


title: 475_array


title: 672_array


title: 470_array


title: 443_array


title: 446_array


title: 441_array


title: 442_array


title: 521_array


title: 423_array


title: 404_array


title: 474_array


title: 267_array


title: 427_array


title: 444_array


title: 394_array

tag: TAA; training set


title: 416_array


title: C100-6 treated with Al for 24h (slide set B) rep. 3

city: Ithaca

first: Lyza

middle: G

last: Maron

state: NY

address: Tower Rd., Cornell University

department: USDA - ARS

institute: Robert W. Holley Center for Agriculture and Health

description:
Cohybridized with GSM260511

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

hyb_protocol: Slides were pre-hybridized for 45 minutes at 42C in 5xSSC, 1%SDS, 1% BSA fraction V. Slides were then washed in water and isopropanol and spin-dried. Slides were hybridized overnight at 42C in 30% formamide, 5xSSC, 0.1%SDS, 5x Denhardts solution, and 0.1 ug/uL polyA RNA. Labeled cDNA was resuspended in 90uL of hybridization buffer and denatured at 95C for 2 minutes before being applied to the slide. Arrays were covered with Lifterslip coverslips (Erie Scientific) and placed in hybridization chambers (Corning). Afer hybridization, slides were washed sequentially once in 1xSSC 0.2%SDS, once in 0.1xSSC 0.2%SDS, and three times in 0.1xSSC. Slides were spin-dried and scanned immediately.

scan_protocol: Slides were scanned in a ScanArray Express scanner (PerkinElmer).

data_processing:
LOWESS normalization was applied.
The LOWESS-normalized signal intensity values were log2 transformed and analyzed by two interconnected ANOVA mixed models using PROC MIXED in SAS (Jin et al., 2001; Wolfinger et al., 2001). The normalization ANOVA model  yij = µ + Ai + Dj + (A x D)ij + eij was applied to account for experiment-wide sources of variation associated with array (Ai, degrees of freedom (df) = 15, random effect), dye (Dj, df = 1, fixed effect), and their interactions. The residuals (eij) were treated as normalized values and analyzed in the following ANOVA model (gene model), where effects were evaluated for each gene individually: rikl = µ + Ai + Gk + Tl + (G x T)kl + ekl. Gk is the kth genotype (i.e. C100-6 or L53; df = 1) and represents the effect of each genotype on the expression of every gene, Tl represents the lth treatment (i.e. 0, 2, 6 or 24 hours of Al treatment; df = 3), and (G x T)kl the interaction between genotype and treatment (df = 3). Array (Ai) was included as a random effect to control for spot effects (Jin et al., 2001). Least square means were calculated, and estimates of differential expression were calculated as the difference between least-square means for each of the terms in the model.

organism: Zea mays

source_name: total RNA pooled from 40 primary roots (apex - 2cm) of maize seedlings (5 days old)

label_protocol: 10ug total RNA was reverse transcribed overnight at 42C using Superscript III (Invitrogen) in the presence of dNTPs and 5-(3-aminoallyl)-UTP. Samples were cleaned-up using Qiaquick PCR Purification kit (Qiagen) and dried on a speed vac. Amino-labeled cDNAs were coupled to Cy dyes using the CyDye Post-Labeling Reactive Dye Pack (Amersham Biosciences). cDNA pellets were resuspended in 0.1M Na2CO3 and allowed to couple to Cy dyes for 2 hours. Reactions were neutralized with 0.1M NaOAc, purified using Qiaquick PCR Purification kit and dried in a speed vac.

growth_protocol: Maize seedlings were germinated in wet filter paper for 3 days, then transferred to a full nutrient solution at pH 4.0 under aeration (Magnacava et al, 1987; Pineros et al, 2005).

extract_protocol: Total RNA was extracted using TRIzol reagent following manufacturer's instructions. RNA was concentrated via NH4Ac/EtOH precipitation

treatment_protocol: The aluminum (Al) treatment was initiated after 24 hours of growth, by replacing the nutrient solution with a solution of the same composition, also containing Al supplied as KAl(SO4)2 to a final free Al3+ activity of 39uM. Root samples were collected at 'time zero', and after 2, 6 and 24 hours of treatment

tag: genotype C100-6 (Al-tolerant), 24h of Al treatment


title: C100-6 treated with Al for 24h (slide set B) rep. 2

description:
Cohybridized with GSM260508

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 391_array


title: 374_array


title: 377_array


title: L53 treated with Al for 6h (slide set B) rep. 2

description:
Cohybridized with GSM260506

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype L53 (Al-sensitive), 6h of Al treatment


title: C100-6 treated with Al for 6h (slide set B) rep. 3

description:
Cohybridized with GSM260504

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype C100-6 (Al-tolerant), 6h of Al treatment


title: L53 treated with Al for 6h (slide set B) rep. 3

description:
Cohybridized with GSM260505

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: L53 treated with Al for 24h (slide set B) rep. 2

description:
Cohybridized with GSM260509

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype L53 (Al-sensitive), 24h of Al treatment


title: C100-6 treated with Al for 6h (slide set B) rep. 2

description:
Cohybridized with GSM260507

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 389_array


title: 368_array


title: 353_array


title: 378_array


title: C100-6 treated with Al for 2h (slide set B) rep. 2

description:
Cohybridized with GSM260500

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype C100-6 (Al-tolerant), 2h of Al treatment


title: C100-6 treated with Al for 2h (slide set B) rep. 3

description:
Cohybridized with GSM260503

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: L53 treated with Al for 2h (slide set B) rep. 3

description:
Cohybridized with GSM260502

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype L53 (Al-sensitive), 2h of Al treatment


title: L53 treated with Al for 2h (slide set B) rep. 2

description:
Cohybridized with GSM260501

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 360_array


title: L53 time zero (slide set B) rep. 2

description:
Cohybridized with GSM260498

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype L53 (Al-sensitive), time zero


title: L53 treated with Al for 24h (slide set B) rep. 3

description:
Cohybridized with GSM260510

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: L53 treated with Al for 6h (slide set B) rep. 1

description:
Cohybridized with GSM260492

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: C100-6 time zero (slide set B) rep. 2

description:
Cohybridized with GSM260499

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.

tag: genotype C100-6 (Al-tolerant), time zero


title: 338_array

description: Gene expression data from peripheral blood of TAA/normal individuals using Applied Biosystems AB1700 Whole Genome Microarray


title: 332_array


title: L53 time zero (slide set B) rep. 3

description:
Cohybridized with GSM260497

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: L53 treated with Al for 24h (slide set B) rep. 5

description:
Cohybridized with GSM260494

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 340_array


title: L53 treated with Al for 2h (slide set B) rep. 5

description:
Cohybridized with GSM260490

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 329_array


title: 333_array


title: 342_array


title: L53 treated with Al for 6h (slide set B) rep. 5

description:
Cohybridized with GSM260495

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 320_array


title: 350_array


title: C100-6 time zero (slide set B) rep. 3

description:
Cohybridized with GSM260496

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: L53 treated with Al for 2h (slide set B) rep. 1

description:
Cohybridized with GSM260493

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 321_array


title: L53 time zero (slide set B) rep. 1

description:
Cohybridized with GSM260488

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 312_array


title: 319_array


title: L53 time zero (slide set B) rep. 5

description:
Cohybridized with GSM260491

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 314_array


title: 324_array


title: 316_array


title: C100-6 treated with Al for 6h (slide set B) rep. 5

description:
Cohybridized with GSM260487

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 310_array


title: C100-6 treated with Al for 2h (slide set B) rep. 1

description:
Cohybridized with GSM260485

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: C100-6 treated with Al for 6h (slide set B) rep. 1

description:
Cohybridized with GSM260484

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: C100-6 treated with Al for 24h (slide set B) rep. 1

description:
Cohybridized with GSM260481

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 304_array


title: 301_array


title: 283_array


title: 298_array


title: 311_array


title: C100-6 time zero (slide set B) rep. 5

description:
Cohybridized with GSM260483

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 2-FH-1-1-26

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

description: The RNA (800ng) samples were labeled by using SuperScript Indirect RNA Amplification System Kit (Invitrogen, cat# L1016-02) based on the method designed by Eberwine y col. 1992. Following RNA amplification (with the incorporation of UTP aminoallil), labeled product was achieved by incubating with Cy3 or Cy5 esters in alkaline media. Dye-swaps were used to correct for differences in incorporation and fluorescent properties of both dyes, generating a number of 9 slides per experiment (three slides for control and three slides for each treatment) with a total number of 18 slides considering technical replicates.  The microarray slides were prehybridized by incubation in 5X SSC, 0.1% SDS, 1% BSA at 42°C.  The next day the cover slip was removed and the slide was washed once in 1X SSC, 0.2% SDS prewarmed to 42°C; once in 0.2X SSC, 0.2% SDS at room temperature; and once in 0.1X SSC at room temperature.  The washes were conduced with gentle shaking at 100 rpm for 5 minutes. Slides were subjected to low speed centrifugation for 2 min at 500 rpm to dry.  The hybridized slides were scanned using a VersArray Chip Reader (BioRad) scanner (two different channels for the two different dyes were used) at three different detector sensitivities.  Images analysis and signal quantification were performed using Spotfinder (free open source software) (www.tm4.org/spotfinder.html), quantifying signal intensity for each spot.  Then, data integration from multiple scanning processes were achieved

data_processing: Background subtraction was performed before calculating ratios.  The elements with either printing or hybridization artifacts were flagged and discarded before analysis.  Only spots with an intensity of at least 1.5 times above the local background in both channels were used for subsequent analysis.  The extracted data from each slide were then log transformed (using log base two) and normalized using two different methods: 3-D normalization (normalization intensity and space dependant) (Alvarez y col, unpublished data) using R package (University of Auckland) R 1.9.0 version (http://www.r-project.org).  Potential artifacts and false positives were eliminated by selecting for further analysis only those clones that exhibited similar expression patterns between the original hybridization and their dye swaps (Yang y col. 2002).  A gene expression matrix was generated and its analysis was focused on genes differentially expressed.  The whole analysis related to gene expression matrix was performed using software Infostat 2006® (Infostat Group, FCA, Córdoba, Argentina).

organism: Helianthus annuus

source_name: Helianthus annuus two-week old seedlings were subjected to 10°C for 24 hours, rep. 3

tag: leaves from two-week old seedlings were subjected to 10°C for 24 hours in pots containing composite soil

source_name: Helianthus annuus control leaf two-week seedlings reference sample (pooled leaves)

tag: leaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24°C temperature) in pots containing composite soil, reference sample (pooled leaves)


title: C100-6 treated with Al for 24h (slide set B) rep. 5

description:
Cohybridized with GSM260486

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: L53 treated with Al for 24h (slide set B) rep. 1

description:
Cohybridized with GSM260489

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 2-FH-1-1-27


title: 263_array

description: Gene expression data from peripheral blood of TAA/normal individuals using Applied Biosystems AB1700 Whole Genome Microarray


title: C100-6 time zero (slide set B) rep. 1

description:
Cohybridized with GSM260480

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 271_array


title: 2-FH-1-1-25

source_name: Helianthus annuus two-week old seedlings were subjected to 10°C for 24 hours, rep. 2


title: C100-6 treated with Al for 2h (slide set B) rep. 5

description:
Cohybridized with GSM260482

Hybridizations were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples co-hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).  See 'Data processing' below.


title: 262_array


title: 2-FH-1-1-22

source_name: Helianthus annuus two-week old seedlings were subjected to 10°C for 24 hours, rep. 1


title: 2-SH-1-1-20

source_name: Helianthus annuus two-week old seedlings watered with 150 mM salt solution for up to 9 hours, rep. 3 (leaves)

tag: leaves from two-week old seedlings watered with 150 mM salt solution for up to 9 hours in pots containing composite soil

tag: leaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24oC temperature) in pots containing composite soil, reference sample (pooled leaves)


title: 2-FH-1-1-24

tag: eaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24°C temperature) in pots containing composite soil, reference sample (pooled leaves)


title: 2-FH-1-1-23


title: 2-SH-1-1-21

tag: eaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24oC temperature) in pots containing composite soil, reference sample (pooled leaves)


title: 286_array


title: 270_array


title: 268_array


title: 288_array


title: 2-SH-1-1-19

source_name: Helianthus annuus two-week old seedlings watered with 150 mM salt solution for up to 9 hours, rep. 2 (leaves)


title: 2-CH-1-1-15

source_name: Helianthus annuus control leaf two-week seedlings rep. 3

tag: leaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24oC temperature) in pots containing composite soil


title: 2-CH-1-1-14

tag: characteristic

value: leaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24oC temperature) in pots containing composite soil