title: BMDM WT3

description:
Slide barcode: 12301881
Image Used: 12301881_2
635nm PMT (volts): 560
PMT (volts): 480
Number of times scanned: 2
Scan date: 21/08/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.


title: D25

status: Public on Sep 12 2007

type: genomic

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

country: Australia

institute: QIMR

description: The 76 melanoma cell lines used in this study were derived from primary cutaneous melanomas or melanoma metastases.

hyb_protocol: The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.

scan_protocol: After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). All genomic positions were based upon hg17 from the UCSC Genome Browser.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanoma Cell Line

label_protocol: The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.

extract_protocol: As per manufacturers protocol using QIAGEN QIamp DNA Blood Maxi Kit

tag: Cell line was was derived from a secondary melanoma tumor with the primary being ina non-CSD body site.


title: D29

tag: Cell line was was derived from a secondary melanoma tumor with the primary being occult.


title: BMDM NF-IL6 KO2

type: RNA

city: Cape Town

first: Anita

middle: R

last: Schwegmann

state: Western Cape

address: Institute for Infectious Diseases and Molecular Medicine, UCT medical School, Anzio Rd, Observatory

department: Division of Infectious Immunology

country: South Africa

institute: Institute for Infectious Diseases and Molecular Medicine, University of Cape Town

description:
University of Cape Town Mouse ID number: UCT51#147
Mouse date of birth: 19/06/2001
Mouse Sex: male
Slide barcode: 12301883
Image Used: 12301883_3
635nm PMT (volts): 620
PMT (volts): 550
Number of times scanned: 3
Scan date: 17/06/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

hyb_protocol: Coverslips (Erie Scientific Company, Portsmouth, NH, USA) were washed in 100% acetone for 1 hour, in 0.2 % SDS for 10 minutes, then twice in double distilled water for 10 minutes for each wash. All wash steps were done at room temperature with gentle agitation. The coverslips were dried in an oven at 42°C for 10 minutes. The MEEBO (Illumina, San Diego, CA, USA) spotted microarrays were printed at the capar Microarray Facility (University of Cape Town, South Africa). The MEEBO array was placed in a hybridisation chamber (ArrayIt, Sunnyvale, CA ,USA) and 200μl pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) added between the array and the coverslip. The Hybridization chamber was sealed and submerged in a plastic container containing water preheated to 42°C. The plastic container was placed in a hybridisation preheated to 42°C and the slides were pre-hybridized for 30 minutes. The slides were washed 5 times in double distilled water. Each wash was done at room temperature for 30-60 seconds. The slides were then dipped in 100% isopropanol and dried by centrifugation in swinging bucket rotor for 5 minutes at 1000 rpm at room temperature. The dried slides were placed in a hybridization chamber and the cleaned hybridization coverslip carefully placed over the array. The microarray slides were used immediately for hybridization. 28μl of the 2 X hybridization buffer pre-heated to 42°C was mixed with the 30μl of the amplified RNA (aRNA) probe mixture. The aRNA probe mixture contained 4ug each of "LM + IFN-y" and untreated aRNA labelled samples. The probe was then heat denatured at 90°C for 3 minutes and then cooled to 42°C. The denatured probe was added very carefully to the pre-hybridized microarray slide at the bottom end of coverslip. Any air bubbles were worked toward the edge by gently tapping the coverslip surface. The hybridization chamber was sealed wrapped in foil to keep out light. The chamber was then submerged in a plastic container containing water tub preheated to 42°C. The hybridization reactions were incubated at 42°C in a hybridization oven for 16-20 hours. The plastic container was also wrapped with foil to retain humidity and block out light. The MEEBO array slide was then washed as follows: the low stringency wash buffer (2 X SSC, 0.1% SDS), medium-stringency wash buffer (1.0X SSC) and high-stringency wash buffer (0.02X SSC) were made fresh. All staining dishes were covered with foil to make them light tight and the laboratory lights were turned off, in order to minimize the exposure of the microarray slides to light. The hybridization chamber was unsealed, the microarray slide gently removed from the chamber. The microarray slide was submerged into a dish containing low stringency wash buffer (2 X SSC, 0.1% SDS) and gently agitated at to remove the coverslip. The microarray slide was washed in the low stringency wash buffer for 4 minutes at room temperature with gentle agitation. The microarray slide was then washed twice in medium stringency wash buffer (1.0X SSC) at room temperature for 4 minutes. The microarray was washed in high-stringency wash buffer (0.02X SSC) slide for each wash. The slides were then dipped 5 times in 100% isopropanol and dried by centrifugation in swinging bucket rotor for 5 minutes at 1000 rpm at room temperature. The slides were kept in a light-tight container and scanned immediately.

scan_protocol: The microarray slides were scanned using an Axon GenePix 4000A (Axon Instruments/Molecular Devices Corporation, Sunnyvale, CA, U.S.A) scanner and GenePix Pro 5.1.0.19 software running on a Windows XP operating system. The scan power was set to 100100, the resolution to 10um and the pixel size to 10. The internal scanner temperature averaged between 37°C to 38°C. The number of lines averaged during the scanning process was set to 2. The microarray slides were scanned at 635nm and 532nm wavelengths and the gene/spot ratios were set for 635nm/532nm. No normalization or background subtraction was done at this stage. The MEEBO microarray slide was initially scanned in the “Preview Mode” to optimise the photo-multiplier (PMT) settings so that the overall fluorescence in the red and green channels were balanced. The channels were considered balanced when the ratio of overall fluorescence in the green and read channels were equal to 1. The microarray slide was then scanned at the optimized PMT settings and the image saved as tiff file. The MEEBO microarray slide was scanned no more than 3 times to avoid damaging the dye molecules resulting in subsequent loss of quantitative florescence data. The array list and grid was loaded over the tiff images using the GenePix 5.1.0.19 software. Individual spots were aligned using the single irregular and /or regular feature tool. Each spot was individually checked for quality and to see if it was aligned to the grid. Spots were flagged as bad if they were (1) printed on top of each other, (2) dilated, (3) looked like doughnuts, (4) were irregular in morphology, (5) had a comet tail or (6) contained particles or scratches. Once the grids were aligned, the settings were saved and the quantitative gene expression data exported as a “GenePix Results” (.gpr) file.

data_processing: Background correction method: probabilistic; Normalization method: print-tip LOWESS and slide scale; the M values in derived from the GenePix results file (.gpr) represent the Cy5/Cy3 intensity ratio. The M values in this sample file represent the treated/untreated sample ratios.

molecule: total RNA

organism: Mus musculus

source_name: BMDM, NF-IL6-deficient (KO) mouse, "LM + IFN-y", 4h

label_protocol: RNA was amplified and labelled as per the manufacturer’s instructions using the Amino Allyl MessageAmp II - Cy3/Cy5 aRNA Amplification Kit from Ambion (Cat #1797).

growth_protocol:
BMDM growth protocol:
After harvesting, the BMDMs were plated at a density of 5 x 10e5 BMDMs/ml in DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin (Gibco, Invitrogen Corporation, Carlsbad, CA, USA) and incubated overnight at 37°C under 5% CO2.
Bacteria growth protocol:
Virulent Listeria monocytogenes (EGD strain) were grown at 37°C in tryptose-soy broth (Difco, Detroit, MI, USA) until early to mid log-phase of growth (OD600=0.2). DMSO was added to a final concentration of 10% and aliquots made and stored at –80°C until use. The titre of the stock was determined checked by plating 100μl of 10-fold serial dilutions of the thawed L. monocytogenes stock on tryptose-soy agar plates. The plates were incubated overnight at 37°C and the next day the number of colonies was counted and the colony forming units (CFU)/ml calculated. Before each infection experiment, a vial was thawed and vortexed (mixed) thoroughly to disperse clumps.

extract_protocol: At 4 hours post-infection the culture supernatant was removed from the BMDM cultures, aliquoted and stored at -80°C. The BMDMs were directly lysed in the culture dish using 1ml TriReagent (Molecular Research Company, Cincinnati, USA) for every 5 x 10e5 BMDMs. Total RNA was extracted from the BMDM lysate using the TriReagent protocol as per the manufacturer’s instructions. The RNA was DNAseI treated and “cleaned up” using the RNeasy RNA Extraction Kit (Qiagen) according to manufacturer’s instructions. This “clean up” step helped remove contaminating genomic DNA, proteins, residual phenol and salts. The elimination of contaminating genomic DNA was confirmed by RT-PCR using primers that bound to genomic DNA. The quality and quantity of the RNA was checked by spectroscopy and denaturing gel electrophoresis. The A260/A280 ratio was measured and an aliquot was run on a 1% agarose gel containing 2.2M formaldehyde. The RNA was stored at –80°C until used.

treatment_protocol:
“LM + IFN-y” refers to BMDMs simultaneously activated with IFN-gamma and infected with L. monocytogenes.
Treatment Protocol:
Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The BMDM monolayers were then simultaneously stimulated with 100U/ml IFN-gamma (BD Pharmigen, BD Biosciences, San Jose, CA, USA) and infected with L. monocytogenes at a multiplicity of infection (MOI) of 10:1 (10 bacilli : 1 macrophage). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml to kill extracellular bacteria.

tag: Bone marrow derived macrophages (BMDMs) were generated in vitro from NF-IL6 KO mouse:

tag: University of Cape Town Mouse ID number

tag: Mouse date of birth

tag: Mouse Sex

value: male

tag: Protocol:

tag: Mice were sacrificed by cervical dislocation and the femur and tibia bones collected. The bone marrow cells were flushed from the bones using DMEM (Gibco, Invitrogen Corporation, Carlsbad, CA, USA) containing 10% FCS, 100U/ml penicillin G and 100μg/ml streptomycin. The cells were washed and concentrated by centrifuging at 1200 rpm at 4°C for 10 minutes. The bone marrow cells were added at a final concentration of 1 x 10e6 cells/ml in PLUTZNIK media (DMEM containing 10% FCS, 5% horse serum, 2mM L-glutamine, 1mM Na-pyruvate, 0.1mM 2-beta-Mercaptoethanol, 30% L929 cell-conditioned medium, 100U/ml penicillin G, 100μg/ml streptomycin) and transferred into a special gas-permeable 15cm x 6cm Teflon coated-bag (Max Planck Institute for Immunobiology, Max Planck, Freiberg, Germany). The L929 conditioned medium contained GM-CSF, which stimulated the differentiation and growth of bone marrow stem cells into macrophages. The open end of the bag was heat-sealed and bone marrow stem cells incubated at 37°C under 5% CO2 for 10 days. The supernatant was discarded and the adherent cells were massaged from the Teflon-coated bags into DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin. The BMDMs were washed twice in DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin to get rid of residual GM-CSF from the L929 conditioned medium. The BMDMs were plated at a density of 5 x 10e5 BMDMs/ml and incubated overnight at 37°C under 5% CO2.

source_name: BMDM,  NF-IL6-deficient (KO) mouse, untreated, 4h

treatment_protocol:
“Untreated” refers to BMDMs that were left untreated (mock control)
Treatment Protocol: Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The "untreated"BMDM monolayers were left untreated and represent mock controls (i.e. they were NOT activated or infected). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml.


title: D22

tag: Cell line derived from a secondary melanoma tumor with the primary tumor being in a non-CSD body site.


title: D17


title: C57BL/10J, pachytene spermatocytes, biological rep1

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Gene expression data from mouse pachytene spermatocytes

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Bioconductor 1.9 and R statistics (version 2.3) using the gcRMA method with default settings and custom chip description file (probes were annotated to Entrez identifiers - NCBI build 36) mm430mmentrezg8, from the Bioconductor repository.

label: biotin

source_name: Mouse pachytene spermatocytes

label_protocol: Between 15 to 40 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Mouse lines used in the experiment were C57BL/10J, C57BL/10J-T43H/T43H and C57BL/10J-T43H/+. All the male mice used in the experiment were two months old.  Mice were euthanized by cervical dislocation and single cell suspension from testicular tubules was prepared.

extract_protocol: Total RNA was isolated from individual populations using RNeasy micro kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Specific spermatogenic cell populations of pre-pachytene spermatocytes, pachytene spermatocytes and spermatids were isolated using fluorescence activated cell sorting of testicular single cell suspension according to ref. (Bastos et al. 2005) with minor modifications.

tag: Genotype

value: C57BL/10J, Gender:male, Age:2 months, Tissue:testes


title: BMDM NF-IL6 KO3

description:
Slide barcode: 12301878
Image Used: 12301878_1
635nm PMT (volts):540
PMT (volts): 450
Number of times scanned: 1
Scan date: 21/08/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

treatment_protocol:
"LM + IFN-y" refers to BMDMs simultaneously activated with IFN-gamma and infected with L. monocytogenes.
Treatment Protocol:
Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The BMDM monolayers were then simultaneously stimulated with 100U/ml IFN-gamma (BD Pharmigen, BD Biosciences, San Jose, CA, USA) and infected with L. monocytogenes at a multiplicity of infection (MOI) of 10:1 (10 bacilli : 1 macrophage). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml to kill extracellular bacteria.

value: female

source_name: BMDM, NF-IL6-deficient (KO) mouse, untreated, 4h

growth_protocol:
BMDM growth protocol:
After harvesting, the BMDMs were plated at a density of 5 x 10e5 BMDMs/ml in DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin (Gibco, Invitrogen Corporation, Carlsbad, CA, USA) and incubated overnight at 37°C under 5% CO2.


title: BMDM WT1

description:
Slide barcode: 12301864
Image Used: 12301864_3
635nm PMT (volts): 610
PMT (volts): 540
Number of times scanned: 3
Scan date: 12/08/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

source_name: BMDM, WT (NF-IL6+/+) mouse, "LM + IFN-y", 4h

source_name: BMDM, WT (NF-IL6+/+) mouse, untreated, 4h


title: BMDM NF-IL6 KO1

description:
Slide barcode: 12301884
Image Used: 12301884_2
635nm PMT (volts): 80
PMT (volts): 610
Number of times scanned:
Scan date:17/08/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

source_name: BMDM,  NF-IL6-deficient (KO) mouse, "LM + IFN-y", 4h

value: female.


title: D20

tag: Cell line was derived from a secondary melanoma tumor with the primary tumor being in a non-CSD body site.


title: NF-κB target gene array in HAECs in response to heat-killed PAO1

status: Public on Sep 08 2007

city: Philadelphia

first: zhe

last: zhang

state: PA

address: 401 Johnson Pavilion, 36th and Hamilton Walk

country: USA

institute: University of Pennsylvania

description:
Detection protocol:
Blocking 15 min
HRP 30ul in 30ml blocking buffer 15 min
Washing in washing buffer 55rpm, 8minX3 times
Detection buffer 30ml for 5 min
ECL reaction 5 min
Exposure 20 sec see strong signals, 40-50 sec see most of the signals, signals last over 20 mins. Using Hyperfilm ECL (Amersham, RPN3114K).

hyb_protocol: Hybridization •	Place the membrane into the bottle (35mm diameter X 150mm), fill bottle with ddH2O and then decant water. •	Add pre-warmed (42C) hybridization buffer 5ml and place in the oven at 42C, rotation12, for 2 hours. •	Add the labeled-cDNA probe to each ottle and hybridize at 42 overnight. •	Wash membranes in the bottles.

scan_protocol: standard, best quality

data_processing: The dots on the array were quantified through densitometric analysis using GeneTools (Syngene, Frederick, MD) and the value of each dot is determined in the equation D = (raw value – background value)/mean value of biotinylated DNA dots. Ratio (Dbacteria: Dcontrol) was used to determine the effect of bacteria stimulation on the gene regulation.

molecule: polyA RNA

source_name: primary human airway epithelial cells

label_protocol:
Preparing labeled cDNA probes:
mRNA                              0.5ug
NFkB primer Mix                 5ul
ddH2O                          add to 10ul final
70C 2 min
42C 2 min
labeling mix                          12 ul
Biotin-dUTP                          2 ul
RTase (Roche#1495062)        1ul
ddH2O                                   5ul
42C 2 min
transfer the later to the former and mix well, 42C 2hours
add 3ul 10Xdenaturing Solution to each sample, 68C 20 min
add 33ul 2Xneutralization Buffer, 72C, 10 min
-20C store

extract_protocol: mRNA of HAECs was isolated using biotin-labeled oligo(dT)20 and streptavidin-conjugated magnetic particles (Roche, Germany).

tag: HAECs at the 5th passage


title: mouse heart 10.5ED VT replicate 1a

city: Charleston

first: Andy

last: Wessels

state: SC

address: 173 Ashley Ave. BSB 648

department: Cell Biology and Anatomy

institute: Medical University of South Carolina

description: Wild type mouse ED10.5-11.0 ventricular region

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: ventricular region

label_protocol: Total RNA (250 ng) was amplified and converted into biotin-labeled cRNA using the RiboAmp® HS RNA Amplification Kit (Arcturus Bioscience, Inc., Mountain View, CA) according to manufacturer recommendations.

extract_protocol: Ventricular regions were microdissected from approximately 80 embryonic day 10.5-11.0 mouse hearts immersed in RNase-free PBS.  The tissue was snap frozen in liquid nitrogen.  Total RNA was extracted using the Qiagen RNeasy MiniKit.

tag: Wild type, C57BL/6, embryonic day 10.5, ventricular region


title: mouse heart 10.5ED AV replicate 1b

description: Wild type mouse ED10.5-11.0 atrioventricular junction

source_name: atrioventricular junction

label_protocol: Total RNA (230 ng) was amplified and converted into biotin-labeled cRNA using the RiboAmp® HS RNA Amplification Kit (Arcturus Bioscience, Inc., Mountain View, CA) according to manufacturer recommendations.

extract_protocol: Atrioventricular junctions were microdissected from approximately 80 embryonic day 10.5-11.0 mouse hearts immersed in RNase-free PBS.  The tissue was snap frozen in liquid nitrogen.  Total RNA was extracted using the Qiagen RNeasy MiniKit.

tag: Wild type, C57BL/6, embryonic day 10.5, atrioventricular junction


title: NF-κB target gene array in HAECs PBS control

tag: primary human airway epithelial cells at the 5th passage


title: D35


title: mouse heart 10.5ED AV replicate 1a


title: D14

tag: Cell line derived from secondary melanoma tumor with the primary being in a non-CSD body site.


title: D04


title: D32


title: D11

tag: Cell line derived from a secondary melanoma tumor with the primary being a mucosal melanoma derived from a non-UV exposed body site.


title: D08

tag: Cell line derived from a secondary melanoma tumor with the primary being in a non-CSD body site.


title: C-32

tag: Cell line derived from a secondary melanoma tumour with the primary being in a non-CSD body site.


title: D05

tag: Cell line derived form secondary melanoma tumor with the primary being in a non-CSD body site.


title: D01

tag: Cell line was derived from a secondary melanoma tumor with the primary tumor being occult.


title: A13

tag: Cell line derived from a secondary melanoma tumor with the primary tumor being in a non-CSD body site


title: A15

tag: Cell line derived from a secondary melanoma tumor with the the primary tumor being in a non-CSD body site


title: mouse heart 10.5ED VT replicate 1b


title: D30

tag: Cell line was was derived from a secondary melanoma tumor with the primary being in a non-CSD body site.


title: AF6

tag: Cell line derived form secondary melanoma tumor with primary tumour being occult


title: D10

tag: Cell line was derived from a secondary melanoma tumor with the primary being an acral tumor from a non-UV exposed body site


title: D03

tag: Cell line was derived from a secondary melanoma tumor with the primary being in a non-CSD body site.


title: A02

tag: Cell Line derived from secondary melanoma tumor with primary tumor located in a non-CSD body site


title: S.cerevisiae Tec1::13myc chIP chip replicate 6 (Slide 76754)

status: Public on Sep 06 2007

city: Urrbrae

first: Anthony

last: Borneman

state: South Australia

address: Paratoo Rd

institute: The Australian Wine Research Institute

hyb_protocol: Nimblegen

scan_protocol: Nimblegen

data_processing: Samples were scanned and with each channel (635 (ch1) and 532 (ch2)) normalized separately according to Nimblegen protocols. log(2) ratios were calculated from these normalized 635 and 532 signals, with Random control spots removed during processing.

organism: Saccharomyces cerevisiae

label_protocol: Klenow random priming (Borneman et al Genes Dev 2006)

growth_protocol: Grown at 30ÁC to OD600 = 0.3 in SD media. Transferred to liquid SLAD for 4 hrs at 30ÁC.

extract_protocol: Chromatin immunoprecipitation (Borneman et al Genes Dev 2006)

tag: S.cerevisiae strain containing Tec1 tagged with 13 myc

source_name: WT control

tag: Wild type S.cerevisiae


title: S.cerevisiae Ste12::13myc chIP chip replicate 5 (Slide 67728)

tag: S.cerevisiae strain containing Ste12 tagged with 13 myc


title: S.cerevisiae Ste12::13myc chIP chip replicate 6 (Slide 76755)


title: S.cerevisiae Ste12::13myc chIP chip replicate 3 (Slide 42196)

growth_protocol: Grown at 30¡C to OD600 = 0.3 in SD media. Transferred to liquid SLAD for 4 hrs at 30¡C.

tag: Sigma1278b diploid strain (825/6 L1) containing Ste12 with C-terminal 13myc tag

tag: Sigma1278b diploid control strain


title: S.mikatae Tec1::13myc chIP chip replicate 1 (Slide 39785)

organism: Saccharomyces mikatae

growth_protocol: Grown at 30ÁC to OD600 = 0.3 in SD media. Transferred to liquid SLAD for 3.5 hrs at 30ÁC.

tag: S.mikatae strain containing Tec1 tagged with 13 myc

tag: Wild type S.mikatae


title: GAF competence slide3

status: Public on Sep 05 2007

city: Nijmegen

first: Peter

last: Burghout

address: Kapittelweg 29

department: Laboratory of Pediatric Infectious Diseases

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: n.v.t.

hyb_protocol: Fluorescently labeled DNA probes were combined and hybridized in Slidehyb buffer 1 (Ambion) to pneumococcal microarrays, which are super-amine glass slides spotted with duplicates of amplicons representing 2,087 S. pneumoniae TIGR4 ORFs and 184 ORFs unique to R6 (PMID: 16787930 ).The microarrays were incubated for 16 hours at 45°C, and then washed with 2xSSC (Invitrogen) containing 0.25% SDS for 5 min, followed by 2 washes in 1xSSC and 0.5xSSC for 5 min each. Finally, slides were dipped into H2O and dried by centrifugation.

scan_protocol: Dual channel array images were acquired on a GenePix 4200AL microarray scanner and analyzed with GenePix Pro software (Axon Instruments, Union City, CA, USA). Spots were screened visually to identify those of low quality.

data_processing: Slide data were processed and normalized using MicroPreP as described (PMID: 15130795). Net signal intensities were calculated using a grid-based background subtraction. Automatically and manually flagged spots and spots with low background-subtracted signal intensity (sum of Cy3 and Cy5 net signals <700) were filtered out of all datasets prior to analysis. DNA microarray data four independent biological replicates and analyzed using a Cyber-T Student’s t test for paired data (PMID: 15130795). The following selection criteria were applied: a minimum of seven reliable measurements, p Bayes < 0.001, and a false-discovery rate (FDR) < 0.05.

organism: Streptococcus pneumoniae R6

source_name: GAF challenged 40,000 CFU mutant library

label_protocol: Chromosomal DNA extracts was digested with AluI (New England Biolabs). The resulting DNA fragments were used as a template for an in vitro T7 RNA polymerase reaction (T7 MegaScript, Ambion). After removal of template DNA by DNAseI treatment, fluorescent Cy3/Cy5-labeled dUTP nucleotides (GE Healthcare) were incorporated by reverse transcription using Superscript III (Invitrogen).

growth_protocol: Growth for ~25 generations with antibiotics

extract_protocol: Chromosomal DNA was isolated from pneumococcal cultures by cetyl-trimethylammonium bromide (CTAB) extraction as described previously (PMID: 8057895).

treatment_protocol: Transformation with antibiotic resistance marker

source_name: GAF initial 40,000 CFU mutant library

growth_protocol: Growth for ~25 generations without antibiotics

tag: GAF initial 40,000 CFU mutant library


title: GAF competence slide1

description: n.v.t.

data_processing: Slide data were processed and normalized using MicroPreP as described (PMID: 15130795). Net signal intensities were calculated using a grid-based background subtraction. Automatically and manually flagged spots and spots with low background-subtracted signal intensity (sum of Cy3 and Cy5 net signals <700) were filtered out of all datasets prior to analysis.  DNA microarray data four independent biological replicates and analyzed using a Cyber-T Student’s t test for paired data (PMID: 15130795). The following selection criteria were applied: a minimum of seven reliable measurements, p Bayes < 0.001, and a false-discovery rate (FDR) < 0.05.

tag: GAF challenged 40,000 CFU mutant library


title: GAF competence slide2

description: n.v.t.


title: S.cerevisiae Ste12::13myc chIP chip replicate 4 (Slide 67729)


title: S.cerevisiae Tec1::13myc chIP chip replicate 4 (Slide 67730)


title: A04

tag: Cell Line derived from secondary tumor with primary located in a non-CSD body site


title: S.mikatae Ste12::13myc chIP chip replicate 3 (Slide 37475)

tag: S.mikatae strain containing Ste12 tagged with 13 myc


title: S.bayanus Ste12::13myc chIP chip replicate 3 (Slide 62329)

organism: Saccharomyces bayanus

growth_protocol: Grown at 30ÁC to OD600 = 0.3 in SD media. Transferred to liquid SLAD for 6 hrs at 30ÁC.

tag: S.bayanus strain containing Ste12 tagged with 13 myc

tag: Wild type S.bayanus


title: S.mikatae Tec1::13myc chIP chip replicate 3 (Slide 63762)


title: Melanoma_123

status: Public on Jun 05 2007

city: boston

first: bin

last: feng

state: MA

address: 44 binney street

institute: dfci

description: expression arrays were used for CGH

hyb_protocol: Genomic DNA hybridization to Agilent CGH arrays were performed as per manufacturer’s protocol (http://www.agilent.com)

scan_protocol: Scanning was performed as per manufacturer's protocol (http://www.agilent.com)

data_processing: LOWESS normalized, background subtracted data obtained from log2 (test/reference). Agilent software was used.

label: cy3, cy5

source_name: Melanoma

label_protocol: Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.

extract_protocol: Total DNA extracted using PureGene kit following manufacturer's instructions (Gentra Systems).

tag: tumor

label: cy5, cy3

source_name: Normal Human DNA

tag: Reference DNA


title: Melanoma_122

description: expression arrays were used for CGH


title: GAF competence slide4

description: n.v.t.


title: Melanoma_119

description: expression arrays were used for CGH


title: Melanoma_121

description: expression arrays were used for CGH


title: Melanoma_120

description: expression arrays were used for CGH


title: S.mikatae Ste12::13myc chIP chip replicate 1 (Slide 37381)


title: S.cerevisiae Ste12::13myc chIP chip replicate 1 (Slide 42415)


title: S.cerevisiae Tec1::13myc chIP chip replicate 3 (Slide 42917)

description: S.cerevisiae Tec1::13myc chIP chip replicate 1

tag: Sigma1278b diploid strain (825/6 L1) containing Tec1 with C-terminal 13myc tag


title: S.mikatae Ste12::13myc chIP chip replicate 2 (Slide 39582)


title: Melanoma_117

description: expression arrays were used for CGH


title: Melanoma_118

description: expression arrays were used for CGH


title: Melanoma_116

description: expression arrays were used for CGH


title: S.mikatae Tec1::13myc chIP chip replicate 2 (Slide 40110)


title: Melanoma_114

description: expression arrays were used for CGH


title: Melanoma_115

description: expression arrays were used for CGH


title: S.bayanus Tec1::13myc chIP chip replicate 3 (Slide 67954)

tag: S.bayanus strain containing Tec1 tagged with 13 myc


title: S.cerevisiae Tec1::13myc chIP chip replicate 5 (Slide 64065)

tag: S.cerevisiae strain containing Tec1 tagged with 13 myc


title: Melanoma_113

description: expression arrays were used for CGH


title: Melanoma_111

description: expression arrays were used for CGH


title: S.bayanus Ste12::13myc chIP chip replicate 1 (Slide 60625)


title: Melanoma_108

description: expression arrays were used for CGH


title: Melanoma_112

description: expression arrays were used for CGH


title: Melanoma_106

description: expression arrays were used for CGH


title: Melanoma_105

description: expression arrays were used for CGH


title: S.cerevisiae Tec1::13myc chIP chip replicate 2 (slide 42141)


title: Melanoma_104

description: expression arrays were used for CGH


title: S.cerevisiae Ste12::13myc chIP chip replicate 2 (slide 42101)


title: Melanoma_109

description: expression arrays were used for CGH


title: S.cerevisiae Tec1::13myc chIP chip replicate 1 (Slide 42138)


title: Melanoma_110

description: expression arrays were used for CGH


title: Melanoma_103

description: expression arrays were used for CGH


title: S.bayanus Tec1::13myc chIP chip replicate 1 (Slide 60495)


title: Melanoma_98

description: expression arrays were used for CGH


title: S.bayanus Tec1::13myc chIP chip replicate 2 (Slide 60622)


title: Melanoma_101

description: expression arrays were used for CGH


title: Melanoma_97

description: expression arrays were used for CGH


title: Melanoma_99

description: expression arrays were used for CGH


title: Melanoma_107

description: expression arrays were used for CGH


title: C.albicans Cph1::13myc chIP chip replicate 2 (Slide 40221)

organism: Candida albicans

growth_protocol: Grown at 25ÁC to OD600 = 0.3 in Lee's media. Transferred to Lee's for 4 hrs at 37ÁC.

tag: Wild type C.albicans

growth_protocol: Grown at 30ÁC to OD600 = 0.3 in Lee's media. Transferred to Lee's for 4 hrs at 37ÁC.

tag: C.albicans strain containing Cph1 tagged with 13 myc


title: C.albicans Cph1::13myc chIP chip replicate 3 (Slide 40113)


title: S.bayanus Ste12::13myc chIP chip replicate 2 (Slide 60540)


title: Melanoma_102

description: expression arrays were used for CGH


title: Melanoma_100

description: expression arrays were used for CGH


title: Melanoma_96

description: expression arrays were used for CGH


title: Melanoma_95

description: expression arrays were used for CGH


title: Melanoma_85

description: expression arrays were used for CGH


title: Melanoma_92

description: expression arrays were used for CGH


title: Melanoma_88

description: expression arrays were used for CGH


title: Melanoma_80

description: expression arrays were used for CGH


title: Melanoma_84

description: expression arrays were used for CGH


title: Melanoma_79

description: expression arrays were used for CGH


title: Melanoma_81

description: expression arrays were used for CGH


title: Melanoma_94

description: expression arrays were used for CGH


title: Melanoma_89

description: expression arrays were used for CGH


title: Melanoma_83

description: expression arrays were used for CGH


title: Melanoma_86

description: expression arrays were used for CGH


title: Melanoma_87

description: expression arrays were used for CGH


title: Melanoma_76

description: expression arrays were used for CGH


title: Melanoma_77

description: expression arrays were used for CGH


title: Melanoma_90

description: expression arrays were used for CGH


title: Melanoma_82

description: expression arrays were used for CGH


title: Melanoma_73

description: expression arrays were used for CGH

data_processing: LOWESS normalized, background subtracted data obtained from log2 (Cy3/Cy5). Agilent software was used.


title: C.albicans Cph1::13myc chIP chip replicate 1 (Slide 39996)


title: Melanoma_71

description: expression arrays were used for CGH


title: Melanoma_72

description: expression arrays were used for CGH


title: Melanoma_78

description: expression arrays were used for CGH


title: Melanoma_74

description: expression arrays were used for CGH


title: Melanoma_70

description: expression arrays were used for CGH


title: Melanoma_75

description: expression arrays were used for CGH


title: Melanoma_69

description: expression arrays were used for CGH


title: Melanoma_68

description: expression arrays were used for CGH


title: Melanoma_66

description: expression arrays were used for CGH


title: Melanoma_67

description: expression arrays were used for CGH


title: Melanoma_91

description: expression arrays were used for CGH


title: Melanoma_65

description: expression arrays were used for CGH


title: Melanoma_57

description: expression arrays were used for CGH


title: Melanoma_58

description: expression arrays were used for CGH


title: Melanoma_56

description: expression arrays were used for CGH


title: Melanoma_64

description: expression arrays were used for CGH


title: Melanoma_55

description: expression arrays were used for CGH


title: Melanoma_63

description: expression arrays were used for CGH


title: Melanoma_59

description: expression arrays were used for CGH


title: Melanoma_61

description: expression arrays were used for CGH


title: Melanoma_54

description: expression arrays were used for CGH


title: Melanoma_53

description: expression arrays were used for CGH


title: Melanoma_49

description: expression arrays were used for CGH


title: Melanoma_52

description: expression arrays were used for CGH


title: Melanoma_50

description: expression arrays were used for CGH


title: Melanoma_51

description: expression arrays were used for CGH


title: Melanoma_47

description: expression arrays were used for CGH


title: Melanoma_46

description: expression arrays were used for CGH


title: Melanoma_45

description: expression arrays were used for CGH


title: Melanoma_44

description: expression arrays were used for CGH


title: Melanoma_42

description: expression arrays were used for CGH


title: Melanoma_41

description: expression arrays were used for CGH


title: Melanoma_40

description: expression arrays were used for CGH


title: Melanoma_43

description: expression arrays were used for CGH


title: Melanoma_38

description: expression arrays were used for CGH


title: Melanoma_39

description: expression arrays were used for CGH


title: Melanoma_32

description: expression arrays were used for CGH


title: Melanoma_34

description: expression arrays were used for CGH


title: Melanoma_35

description: expression arrays were used for CGH


title: Melanoma_31

description: expression arrays were used for CGH


title: Melanoma_36

description: expression arrays were used for CGH


title: Melanoma_26

description: expression arrays were used for CGH


title: Melanoma_29

description: expression arrays were used for CGH


title: Melanoma_33

description: expression arrays were used for CGH


title: Melanoma_37

description: expression arrays were used for CGH


title: Melanoma_30

description: expression arrays were used for CGH


title: Melanoma_24

description: expression arrays were used for CGH


title: Melanoma_27

description: expression arrays were used for CGH


title: Melanoma_23

description: expression arrays were used for CGH


title: Melanoma_25

description: expression arrays were used for CGH


title: Melanoma_28

description: expression arrays were used for CGH


title: Melanoma_93

description: expression arrays were used for CGH


title: Melanoma_15

description: expression arrays were used for CGH


title: Melanoma_17

description: expression arrays were used for CGH


title: Melanoma_16

description: expression arrays were used for CGH


title: Melanoma_19

description: expression arrays were used for CGH


title: Melanoma_21

description: expression arrays were used for CGH


title: Melanoma_14

description: expression arrays were used for CGH


title: Melanoma_18

description: expression arrays were used for CGH


title: Melanoma_20

description: expression arrays were used for CGH


title: Melanoma_13

description: expression arrays were used for CGH


title: Melanoma_22

description: expression arrays were used for CGH


title: Melanoma_11

description: expression arrays were used for CGH


title: Melanoma_9

description: expression arrays were used for CGH


title: Melanoma_8

description: expression arrays were used for CGH


title: Melanoma_12

description: expression arrays were used for CGH


title: Melanoma_7

description: expression arrays were used for CGH


title: Melanoma_10

description: expression arrays were used for CGH


title: Melanoma_2

description: expression arrays were used for CGH


title: Melanoma_6

description: expression arrays were used for CGH


title: Melanoma_1

description: expression arrays were used for CGH


title: Melanoma_3

description: expression arrays were used for CGH


title: Melanoma_4

description: expression arrays were used for CGH


title: Melanoma_60

description: expression arrays were used for CGH


title: Melanoma_5

description: expression arrays were used for CGH


title: Colon_81

description: expression arrays were used for CGH

source_name: Colon


title: Colon_79

description: expression arrays were used for CGH


title: Colon_75

description: expression arrays were used for CGH


title: Colon_77

description: expression arrays were used for CGH


title: Colon_76

description: expression arrays were used for CGH


title: Colon_80

description: expression arrays were used for CGH


title: Colon_71

description: expression arrays were used for CGH


title: Colon_70

description: expression arrays were used for CGH


title: Colon_74

description: expression arrays were used for CGH


title: Colon_72

description: expression arrays were used for CGH


title: Colon_73

description: expression arrays were used for CGH


title: Colon_69

description: expression arrays were used for CGH


title: Melanoma_48

description: expression arrays were used for CGH


title: Colon_78

description: expression arrays were used for CGH


title: Colon_62

description: expression arrays were used for CGH


title: Colon_63

description: expression arrays were used for CGH


title: Colon_67

description: expression arrays were used for CGH


title: Colon_66

description: expression arrays were used for CGH


title: Colon_64

description: expression arrays were used for CGH


title: Colon_60

description: expression arrays were used for CGH


title: Colon_65

description: expression arrays were used for CGH


title: Colon_68

description: expression arrays were used for CGH


title: Colon_55

description: expression arrays were used for CGH


title: Colon_59

description: expression arrays were used for CGH


title: Colon_58

description: expression arrays were used for CGH


title: Colon_57

description: expression arrays were used for CGH


title: Colon_61

description: expression arrays were used for CGH


title: Colon_54

description: expression arrays were used for CGH


title: Colon_53

description: expression arrays were used for CGH


title: Colon_51

description: expression arrays were used for CGH


title: Colon_52

description: expression arrays were used for CGH


title: Colon_48

description: expression arrays were used for CGH


title: Colon_49

description: expression arrays were used for CGH


title: Colon_45

description: expression arrays were used for CGH


title: Colon_46

description: expression arrays were used for CGH


title: Colon_50

description: expression arrays were used for CGH


title: Colon_44

description: expression arrays were used for CGH


title: Colon_47

description: expression arrays were used for CGH


title: Melanoma_62

description: expression arrays were used for CGH


title: Colon_41

description: expression arrays were used for CGH


title: Colon_42

description: expression arrays were used for CGH


title: Colon_28

description: expression arrays were used for CGH


title: Colon_43

description: expression arrays were used for CGH


title: Colon_37

description: expression arrays were used for CGH


title: Colon_36

description: expression arrays were used for CGH


title: Colon_39

description: expression arrays were used for CGH


title: Colon_38

description: expression arrays were used for CGH


title: Colon_32

description: expression arrays were used for CGH


title: Colon_40

description: expression arrays were used for CGH


title: Colon_33

description: expression arrays were used for CGH


title: Colon_35

description: expression arrays were used for CGH


title: Colon_34

description: expression arrays were used for CGH


title: Colon_30

description: expression arrays were used for CGH


title: Colon_25

description: expression arrays were used for CGH


title: Colon_31

description: expression arrays were used for CGH


title: Colon_26

description: expression arrays were used for CGH


title: Colon_17

description: expression arrays were used for CGH


title: Colon_22

description: expression arrays were used for CGH


title: Colon_29

description: expression arrays were used for CGH


title: Colon_23

description: expression arrays were used for CGH


title: Colon_21

description: expression arrays were used for CGH


title: Colon_18

description: expression arrays were used for CGH


title: Colon_1

description: expression arrays were used for CGH


title: Colon_12

description: expression arrays were used for CGH


title: Colon_27

description: expression arrays were used for CGH


title: Colon_24

description: expression arrays were used for CGH


title: Colon_11

description: expression arrays were used for CGH


title: Colon_13

description: expression arrays were used for CGH


title: Colon_15

description: expression arrays were used for CGH


title: Colon_2

description: expression arrays were used for CGH


title: Colon_16

description: expression arrays were used for CGH


title: Colon_8

description: expression arrays were used for CGH


title: Colon_14

description: expression arrays were used for CGH


title: Colon_3

description: expression arrays were used for CGH


title: Colon_6

description: expression arrays were used for CGH


title: Colon_7

description: expression arrays were used for CGH


title: Colon_4

description: expression arrays were used for CGH


title: Colon_10

description: expression arrays were used for CGH


title: Colon_5

description: expression arrays were used for CGH


title: TALL_18

description: Tall tumor sample compared to normal human DNA sample

source_name: TALL tumor


title: Colon_9

description: expression arrays were used for CGH


title: Colon_56

description: expression arrays were used for CGH


title: TALL_17


title: TALL_11


title: TALL_15


title: Colon_19

description: expression arrays were used for CGH


title: TALL_10


title: TALL_9


title: TALL_14


title: TALL_7


title: TALL_3


title: TALL_2


title: TALL_6


title: GBM_38

description: Human GBM sample compared to Normal Human DNA

source_name: GBM


title: TALL_16


title: TALL_8


title: TALL_12


title: GBM_36


title: TALL_4


title: GBM_34


title: TALL_13


title: GBM_35


title: GBM_33


title: GBM_37


title: TALL_5


title: GBM_31


title: GBM_32


title: GBM_30


title: Colon_20

description: expression arrays were used for CGH


title: TALL_1


title: GBM_29


title: GBM_26


title: GBM_28


title: TALL_26


title: GBM_27


title: GBM_25


title: TALL_25


title: GBM_24


title: TALL_23


title: GBM_22


title: GBM_23


title: GBM_21


title: TALL_20


title: GBM_17


title: TALL_24


title: GBM_20


title: GBM_18


title: TALL_19


title: GBM_15


title: GBM_13


title: GBM_16


title: GBM_14


title: Lymphoma_TKO_10 (GPL4092)

description: Lymphoma sample from Atm-/-, mTerc-/-, p53-/- triple knock-out mice and reference DNA from a matched mouse of the same tumorsample were analyzed.

source_name: Atm-/-,mTerc-/-,p53-/- mouse lymphoma

tag: Strain:C57BL/6; lymphoma

source_name: matched normal to ch1


title: Lymphoma_TKO_13 (GPL4092)


title: Lymphoma_TKO_12 (GPL4092)


title: Lymphoma_TKO_11 (GPL4092)


title: GBM_10


title: GBM_11


title: GBM_19


title: Lymphoma_TKO_9 (GPL4092)


title: Lymphoma_TKO_8 (GPL4092)


title: TALL_21


title: GBM_12


title: GBM_8


title: GBM_9


title: Lymphoma_TKO_7 (GPL4092)


title: Lymphoma_TKO_6 (GPL4092)


title: GBM_6


title: Lymphoma_TKO_5 (GPL4092)


title: Lymphoma_TKO_4 (GPL4092)


title: GBM_4


title: Lymphoma_TKO_3 (GPL4092)


title: TALL_22


title: Lymphoma_TKO_2 (GPL4092)


title: Lymphoma_TKO_18

description: lymphoma sample from Atm-/-, mTerc-/-, p53-/- triple knock-out mice were compared to 3 week old thymus RNA from healthy mice of p53 Hets

hyb_protocol: RNA hybridization to Agilent CGH arrays were performed as per manufacturer’s protocol (http://www.agilent.com)

label_protocol: Labeling to Agilent CGH arrays were performed as per manufacturer’s protocol (http://www.agilent.com)

extract_protocol: RNA was prepared by an initial extraction with Trizol (Invitrogen) according to the manufacturer’s instructions.  Pelleted total RNA was then digested with RQ1 DNase (Promega) and subsequently purified through RNA purification columns (Gentra).

source_name: normal mouse reference


title: GBM_7


title: GBM_2


title: Lymphoma_TKO_17


title: Lymphoma_TKO_1 (GPL4092)


title: Lymphoma_TKO_16


title: GBM_5


title: GBM_3


title: Lymphoma_TKO_22 (GPL2884)

description: Lymphoma samples from Atm-/-, mTerc-/-, p53-/- triple knock-out mice are compared to reference DNA from healthy mice of the same line.


title: Lymphoma_TKO_20 (GPL2884)


title: Lymphoma_TKO_15


title: Lymphoma_TKO_14


title: Lymphoma_TKO_21 (GPL2884)


title: PDAC_29

description: Human pancreas tumor sample versus normal human DNA sample were analyzed.

source_name: Human Pancreas Tumor Sample


title: GBM_1


title: Lymphoma_TKO_13


title: Lymphoma_TKO_19 (GPL2884)


title: PDAC_30


title: Lymphoma_TKO_18 (GPL2884)


title: PDAC_26


title: PDAC_27


title: PDAC_28


title: Lymphoma_TKO_16 (GPL2884)


title: Lymphoma_TKO_17 (GPL2884)


title: Lymphoma_TKO_11


title: PDAC_25


title: PDAC_23


title: Lymphoma_TKO_13 (GPL2884)


title: Lymphoma_TKO_9


title: PDAC_24


title: Lymphoma_TKO_10


title: Lymphoma_TKO_12 (GPL2884)


title: PDAC_21


title: Lymphoma_TKO_8


title: Lymphoma_TKO_6


title: Lymphoma_TKO_14 (GPL2884)


title: PDAC_22


title: Lymphoma_TKO_11 (GPL2884)


title: Lymphoma_TKO_10 (GPL2884)


title: Lymphoma_TKO_4


title: PDAC_18


title: Lymphoma_TKO_5


title: PDAC_19


title: Lymphoma_TKO_9 (GPL2884)


title: Lymphoma_TKO_12


title: Lymphoma_TKO_8 (GPL2884)


title: PDAC_20


title: PDAC_16


title: Lymphoma_TKO_1


title: PDAC_17


title: Lymphoma_TKO_5 (GPL2884)


title: Lymphoma_TKO_2


title: Lymphoma_TKO_3 (GPL2884)


title: PDAC_15


title: Lymphoma_TKO_1 (GPL2884)


title: Lymphoma_TKO_6 (GPL2884)


title: PDAC_13


title: Lymphoma_TKO_4 (GPL2884)


title: Lymphoma_TKO_3


title: Lymphoma_TKO_2 (GPL2884)


title: PDAC_9


title: PDAC_11


title: Lymphoma_TKO_7 (GPL2884)


title: PDAC_12


title: PDAC_7


title: PDAC_14


title: PDAC_10


title: PDAC_8


title: PDAC_6


title: PDAC_5


title: PDAC_3


title: PDAC_4


title: Small RNAs from Arabidopsis AGO4 complex

status: Public on Feb 21 2007

city: Cold Spring Harbor

first: Gregory

middle: J.

last: Hannon

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: Small RNAs that are associated with Arabidopsis AGO4 complex

data_processing: The small RNA sequences were mapped to the Arabidopsis genome provided by TIGR (release version 5) using Perl scripts

organism: Arabidopsis thaliana

source_name: Purified Arabidopsis AGO4 complex

extract_protocol: Small RNAs were extracted using Trizol reagent from TAP-purified AGO4 complex


title: Lymphoma_TKO_15 (GPL2884)


title: PDAC_2


title: CH1812

status: Public on Dec 01 2005

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the Neurointermediate lobe of the Pituitary from 5 control animals

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

organism: Rattus norvegicus

source_name: Neurointermediate lobe _control

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit  (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

tag: Strain

value: Sprague Dawley

tag: Gender

value: Male

tag: Age

value: 10-12 weeks

tag: Tissue

value: Neurointermediate lobe of the Pituitary


title: CH1813


title: CH1811


title: CH1814


title: CH2222

description: Sample represents the Paraventricular nucleus from 5 control animals

source_name: Paraventricular nucleus_control

value: Hypothalamic Paraventricular nucleus


title: Lymphoma_TKO_7


title: PDAC_1


title: gk465_vs_N2

status: Public on Nov 18 2006

city: Vancouver

first: Donald

last: Moerman

state: British Columbia

address: 301 - 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) . see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: The raw log2 intensity ratio were normalized with the LOESS regression

organism: Caenorhabditis elegans

source_name: C. elegans mutant gk465

label_protocol: Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.

tag: Strain gk465

tag: Hermaphrodites

tag: whole animals

source_name: C. elegans wild isolate N2

tag: Strain N2


title: CH2127


title: CH1810


title: CH2128


title: gk462_vs_N2

hyb_protocol: see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

source_name: C. elegans mutant gk462

tag: Strain gk462


title: gk460_vs_N2

source_name: C. elegans mutant gk460

tag: Strain gk460


title: Males_vs_N2

source_name: C. elegans Males (XO)

tag: Males

label_protocol:
The scanner used was an Axon Scanner (Model # 4000B) .
see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.


title: VC615_vs_N2 mixed

source_name: C. elegans mutant VC615

label_protocol:
The scanner used was an Axon Scanner (Model # 4000B) .
see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319

tag: Strain VC615


title: gk463_vs_N2

source_name: C. elegans mutant gk463

tag: Strain gk463


title: Bacterium_GVE2-infected_4h_rep3

status: Public on Aug 26 2006

city: xiamen

first: xiaobo

address: No. 178 Daxue Rd.,

country: China

institute: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration,China

description: Eight DNA fragments from yeast genome and a randomly synthesized DNA fragment (Hex) were included as exogenous positive controls to normalize the microarry date. Distilled water was used as negative controls; The cDNAs from uninfected Geobacillus sp. E263 were labeled with Cy5 and the cDNAs from phage-infected Geobacillus sp. E263 labeled with Cy3. At the same time, the cDNAs from yeast and the Hex DNA were labeled with Cy3.

data_processing: log ratio (4h/dui)

organism: Geobacillus sp. E263

source_name: GVE2-infected Geobacillus sp. E263

tag: Thermophilic Geobacillus sp. E263 was isolated from an east-Pacific hydrothermal field (12°42’29’’N, 104°02’01’’W) at a depth of 3083 m in our laboratory

source_name: uninfected Geobacillus sp. E263


title: C. jejuni (agar vs broth) - dataset 4

status: Public on Jul 29 2005

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

institute: National Research Council

description: Growth in broth was achieved by transferring stock culture to MH broth in tissue culture flasks and incubated microaerobically. Growth on agar was achieved by transferring stock culture onto MH agar plates, spreading the culture to produce a lawn, and incubation microaerobically. Cell densities in both growth conditions increased steadily up to 12 hrs and maximum cell densities were achieved at 18 hrs following which cell death starts to occur. Thus based on the growth curve C. jejuni cells at 16 hrs of incubation were used in all studies.

data_processing: ArrayPro Analyser

organism: Campylobacter jejuni

source_name: C. jejuni 11168 grown on agar

tag: C. jejuni 11168 grown on agar

source_name: C. jejuni grown in broth

tag: C. jejuni grown in broth


title: VC615_vs_N2 heterozygous


title: VC766_vs_N2

source_name: C. elegans mutant VC766

label_protocol: Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol.  Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5.  1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes.  10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet.  Samples were centrifuged and incubated at 37 ºC for 2 hours.  10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction.  DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes.  The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol.  After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water.  DNA concentration was measured using a spectrophotometer.

tag: Strain VC766


title: Hawaiian_vs_N2

source_name: C. elegans wild isolates CB4856

tag: Hawaiian strain CB4856


title: Madeira_vs_N2

source_name: C. elegans wild isolates JU258

tag: Madeira wild strain JU258


title: VC100_vs_N2

source_name: C. elegans mutant VC100

tag: Strain VC100

tag: Whole animals


title: C. jejuni (agar vs broth) - dataset 2

label: C. jejuni grown in broth


title: C. jejuni (agar vs broth) - dataset3


title: Aerobic nitrogen limited 2

status: Public on Sep 03 2004

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description:
M26
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner..

data_processing:
Data Acquisition and Primary Analysis—Acquisition and quantification
of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

label: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)

source_name: chemostat culture

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level.. For nitrogen-limited, the composition was 1.0 g of (NH4)2SO4, 5.3 g of K2SO4, 3.0 g of KH2PO4, 0.5 g of MgSO4_7H2O, and 59 g of glucose.

extract_protocol:
Sampling and RNA Isolation—
Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40–60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).

treatment_protocol: Liquid nitrogen quenching

tag: Strain and Maintenance

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: gk488_vs_N2

source_name: C. elegans mutant gk488

tag: Strain gk488

tag: Hermaphrodites

tag: whole animals


title: CH2125

source_name: Paraventricular nucleus_control

tag: Strain

tag: Gender

tag: Age

tag: Tissue


title: C. jejuni (agar vs broth) - dataset 1

source_name: C. jejuni 11168 grown on agar.

tag: C. jejuni 11168 grown on agar.


title: gk487_vs_N2

source_name: C. elegans mutant gk487

tag: Strain gk487

source_name: C. elegans wild isolate N2

tag: Strain N2


title: CH2126


title: PC-346C Casodex Treated Cells at 48h - biological rep 1

status: Public on Sep 15 2007

city: Notre Dame

first: Randy

last: Jeffrey

state: IN

address: Rm 232, Galvin Life Sciences Bldg

department: Biological Sciences

institute: University of Notre Dame

description: Gene expression data from PC-346C prostate cancer cells treated with vehicle control for 48h

hyb_protocol: Refer to Nimblegen Systems Inc

scan_protocol: Refer to Nimblegen Systems Inc

data_processing: RMA normalized data sets provided by Nimblegen Systems Inc were analyzed using GeneSpring (Agilent)

label: Refer to Nimblegen Systems Inc

source_name: Casodex (50uM) treated PC-346C cells harvested after 48h of incubation

label_protocol: Refer to Nimblegen Systems Inc

growth_protocol: PC-346C prostate cancer cells were plated at a density of three million cells per 150cm2 dish in 25mL of DMEM/F-12 medium supplemented with 2% Charcoal Stripped Serum, ITS-G, testosterone, EGF, Hydrocortisone, T3, phosphoethanolamine, Fibronectin, Fetuin, cholera toxin and PenStrep and incubated for 36h prior to treatment

extract_protocol: Qiagen Rneasy extraction protocol according to manufacturer's instuctions.

treatment_protocol: 150cm2 dishes containing PC-346C cells were treated with 50uM Casodex (75% EtOH and 25%DMSO - Carrier) following a 24h incubation period after initial plating

tag: PC-346C prostate cancer cells