title: MS_HCT116_p53+_48h_50uM_AAI_R2

status: Public on Jul 28 2008

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 50% formamide, amersham hyb buffer, 3 nights, 42 degrees

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 ul hybridisation mix (19 ul Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150ul aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000A. Voltage: 3.06 3.54. Resolution (micrometers): 10.

data_processing: Regions were used for normalizing samples 1-54. 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.

label_protocol: Total RNA (4 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Cell pellets were collected and total RNA extracted using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK). After addition of lysis buffer (RLT, Qiagen) samples were homogenized using QIAshredders (Qiagen).

tag: tissue type

value: tumor


title: No respiratory symptoms (Viro3P11-012)

status: Public on Jul 09 2008

type: RNA

city: San Francisco

first: Joe

last: DeRisi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: University of California, San Francisco

description: RdABC amplified RNA from Nasal Lavage

hyb_protocol: standard overnight hybridization

scan_protocol: Axon 4000 scanner

data_processing: Median feature intensity minus median background intensity. The data analysis software used is E-Predict, which normalizes the data using a variety of measures: sum, quadratic, unit-vector, or no normalization (please see Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck  S, Wang D, DeRisi JL.E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.Genome Biol. 2005;6(9):R78. Epub 2005 Aug 30).  E-Predict is public access.  For the purposes of this paper, sum-normalized intensities were used in the analysis.

molecule: total RNA

organism: Viruses

source_name: RdABC amplified RNA from Nasal Lavage

label_protocol: Rd C Cy3 incorporation

extract_protocol: RNeasy followed by DNAse treatment

tag: No respiratory symptoms


title: Upper respiratory tract infection (Viro3P11-016)

description: probe 70 oligo

source_name: probe 70 oligo

tag: Upper respiratory tract infection


title: No respiratory symptoms (Viro3P11-015)

description: probe 70 oligo


title: Bronchiolitis (Viro3P10-256)

description: RdABC amplified RNA from Nasal Lavage

tag: Bronchiolitis


title: Bronchiolitis (Viro3P11-042)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-261)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-018)

description: probe 70 oligo


title: 13130786_sce15cy3_sce16cy5

city: Mississauga

first: James

middle: B

last: Anderson

state: Ontario

address: 3359 Mississauga Road N.

department: Biology

country: Canada

institute: University of Toronto

description:
Isopropanol precipitation
_ Add 1 volume (I added 120 µL) of isopropanol.
_ Precipitate the DNA on at -20C for 30 minutes (or place at –20°C); spin 10 minutes at 4°C. _ Remove isopropanol from pellet; rinse pellet with ice cold 70% ethanol (200ul). Scott rinses twice in 70% EtOH, the second time with EtOH that has been sitting at RT.
_ Pulse centrifuge the samples, and remove all remaining alcohol by pipetting.
_ Do not allow the labeled cDNA to dry completely.
Resuspend the pellet in 5 ul of dH2O (SigmaW4502).
Often, some colour can be observed in the resuspended pellet; however, lack of colour does not necessarily indicate a failed reaction.

hyb_protocol: Hybridization A prehybridization step is not required. Although the best results are generally obtained from using the cDNA immediately after labeling, it can be stored in the dark at –20°C for several days. _ To each 100 µL of DIG Easy Hyb solution (Roche), add 5 µL of yeast tRNA (Invitrogen; 10 mg/ml) and 5 µL of calf thymus DNA (Sigma; 10 mg/ml). (I used ss salmon sperm DNA 10mg/ml). _Incubate the mixture at 65°C for 2 minutes and cool to room temperature. Add 77.5ul of DIG easy Hyb soln to each pooled pair of Cyanine 5 and Cyanine 3-labeled cDNA (about 5 µL). Pipette well to mix. _Incubate at 65°C for 3 minutes, and cool to room temperature. Vortex and quick spin. _prewarm the hyb chamber and container with SDW.37C. _ For the hybridizations involving the use of coverslips, the hyb mixture should be pipetted directly onto the coverslip. Place coverslip onto a reliable surface (the corner of a tip box works well) and add the hyb mixture. Lay the slide “array-side” down on top of the coverslip. Use a 24 x 50 mm coverslip for the yeast arrays. _ Carefully place the slide(s) into hybridization chamber(s). The hybridization chambers that we use are plastic microscope slide boxes containing a small amount of DIG Easy Hyb solution in the bottom (to keep a humid environment). Clean plain microscope slides are placed at every second or third slide position in the slide box to create rails or a platform onto which the hybridization arrays can be placed. Each hybridization chamber can hold two or three hybridization slides (depending on which direction the slides are placed). The lid is carefully placed onto the box and the box is then wrapped with plastic wrap. _ Incubate on a level surface in a 37 °C incubator overnight (about 18 hours). Washing _ Critical that gloves be worn during this procedure _Disassemble the hybridization chamber and remove the coverslip by quickly but gently dipping the array in 1X SSC (let the coverslip slide off gently, let the CV slide off gently). _ When all of the arrays have been removed from the hybridization chambers, wash 3 times for 15 minutes each at 50°C in 50 ml Falcon tubes containing pre-warmed (at 50oC) 1X SSC/0.1% SDS with gentle occasional agitation. I wash 2 slides per falcon tube back to back for all washes except the very last one before scanning. _After the washes are complete, rinse the slides twice in room temperature 1X SSC (plunging 4-6 times) and then in 0.1X SSC. The last wash is the most stringent for the array so do this wash at the last minute before scanning. Shake vigorously in this wash, do not be afraid of washing off the dyes in this step, it is critical for removing background. Also must use fresh 0.1X SSC for each slide. _ I dry the slides from the last wash in the Westwood lab with the pressurized air sprayer. _ Arrays should be stored in the dark. It is recommended that arrays be scanned as soon as possible after they are washed.

scan_protocol: Scanning and data analysis Microarrays were scanned at a 10-µm resolution with a ScanArray 4000 system (GSI Lumonics/Perkin Elmer), using both blue and red lasers. The 16-bit TIFF images were saved and quantified with QuantArray software (v3.0, Perkin Elmer). The adaptive quantification algorithm was used. Further analysis, including data normalization, was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.). The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess (Locally Weighted Scatter Plot Smoother) normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100.

data_processing:
Normalization
This method normalizes the data to the intensity for each spot and its surrounding area. This method compensates for the effects of dim spots and ensures that normalization is not influenced by the absolute values or the distribution of the bright spots. This method compares the channel 2 intensity /channel 1 intensity normalized (treated/over normalized reference sample) for all non flagged spots in each sub grid (Reference Gene traffic 2.8 Duo Manual Rev. C).
Once the data was normalized the criteria used for filtering the microarray data and selection of significantly unregulated or down regulated genes were for each gene the mean log 2 ratio up 0.67 for all valid spots of that gene. Coefficient of variance for all valid spots of that gene less than 1, Number of valid spots greater at 75% for the gene. The covariance of Variance is the standard deviation expressed as a percentage of the mean. This is a measure of the precision of the outcome over several replications. The higher the precision the lower the covariance so that outliers are not counted in the results as valid data spots.
Usable spot pairs were identified. (Usable spot pairs were defined as having the signal intensities of each channel greater than twice the average background for that channel and having the fluorescence intensity of at least one channel greater than the average intensity of the background.) The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100. The three hybridizations were treated as replicates, and a distribution of the mean log2-transformed ratios of the Cy5/Cy3 intensities was plotted (Fig. 4, dotted line). For replicate experiments, at least two-thirds of the spots for a 4) had to meet the aforementioned validation criteria for thegiven gene (n ≥ ratio to be included in the distribution. For 95% of the data, the average fold change between the two channels was less than 1.2. Over 99% of the spots exhibited Cy3 and Cy5 signal intensities within ±1.3-fold of each other. The average number of usable spot pairs per slide in these trials was 5542.
Genes were considered in the analysis only if the covariance of the aggregate data from all six arrays was less than 100%.

organism: Saccharomyces cerevisiae

source_name: Sce15, reference

label_protocol:
Protocols from the UHN Microarray Centre 2003.05.15 ©2003 University Health Network/Ontario Cancer Institute
Direct Labeling Protocol from the University Health Network (UHN) Microarray Centre
RNA Isolation
There are a variety of protocols available that will yield RNA of sufficient quality for microarrays. Many microarray users rely on the Qiagen RNeasy kit for the isolation or cleanup of total RNA. We have not observed any appreciable difference between images derived from the use of total RNA versus mRNA.
Determine the final concentration of purified RNA by measuring A260 and A280. Prepare RNA to a final concentration of at least 1 µg/µL.
I used the hot phenol/chloroform protocol from this website site: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
Reverse Transcription
For 10-20 µg of Qiagen purified total RNA or 0.1-0.5 µg of mRNA, the RT reaction volume is 40 µl. I aimed for 20ug.
Combine the following on ice:
8.0 µL 5X First Strand reaction buffer (Superscript II, Invitrogen)
1.5 µL AncT mRNA primer (5’-T20VN, 100 pmol/_l)
3.0 µL dNTP (-dCTP) (6.67 mM each of dATP, dGTP, dTTP)
1.0 µL 2 mM dCTP
1.0 µL 1 mM Cyanine 3 or Cyanine 5-dCTP (NEN)
4.0 µL 0.1 M DTT
0.1 – 20 µg RNA (0.1-0.5 µg mRNA or 10-20 µg total RNA)
to 40 µL dH20 (Sigma)
_ Label the two different samples to be analyzed (i.e. control and experimental) on an array with different fluors (i.e. Cyanine 3 or Cyanine 5). It is also suggested that you perform reciprocal labeling (For more information on reciprocal labeling see the microFAQ).
_ Incubate the labeling reaction at 65°C for 5 minutes, then at 42°C for 5 minutes. Ensure that the reactions are kept in the dark as the dyes are light sensitive. If the incubator is not covered use aluminum foil to create a cover preventing light from photo bleaching the fluors.
_ Add 2 µL of reverse transcriptase (Superscript II, Invitrogen). Incubate at 42 °C for 3 hours.
Stop Reaction
_ Briefly centrifuge the reaction and place on ice.
_ Add 5 µL of 50 mM EDTA (pH 8.0), and 4 µL of 5 N NaOH. Mix well by pipetting
_ Incubate at 65°C for 20 minutes to hydrolyse the RNA.
_ Add 4.5 µL of 5 M acetic acid. (A small aliquot of the reaction can be pipetted onto pH paper to ensure the solution is neutralized. Checking the pH is also an optional step that is not necessary for every reaction.)
_ Combine the two reactions that will be hybridized to the same slide (i.e. control and experimental). (I added Cy5 to Cy3).

growth_protocol: Evolved in 0.5x YPD. 57 days of growth, 1 transfer per day, No drug

extract_protocol:
Reference for this protocol: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
This is a standard Yeast hot acid phenol/chloroform RNA extraction protocol followed by a total RNA clean up using Qiagen RNeasy mini spin columns. The RNA is then quantified by measuring A260 and A280 and then checked by running a DEPC 1% Agarose gel.
RNA extraction:
1. Centrifuge cells at room temperature, wash with sterile water and centrifuge again. Usually, 50ml of culture at OD 0.6-0.8 are enough.
2. If necessary, store cell pellets at -80°C.
3. Resuspend cell pellets in TES buffer (10mM Tris pH 7.5, 10mM EDTA, 0.5%SDS, autoclaved) (1.2ml buffer for 50 OD of cells).
4. Transfer 400ul aliquots of the resuspended cells in three 1.5ml eppendorf tubes.
5. Add 400ul of Phenol:Chloroform 5:1 (from Sigma ref: P-1944).
6. Incubate at 65°C for 20min and vortex 30sec every 5min (be very careful with hot phenol!!).
7. Cool at -80°C for 30min.
8. Centrifuge at room temperature for 15min at 15000rpm.
9. Keep the aqueous phase and add 400ul of Phenol:Chlorofom 5:1.
10. Vortex tubes three times for 30sec then centrifuge.
Repeat steps 8 to 10 one more time.
11. Add 300µl of Chloroform (ready red from Sigma) to the aqueous phase.
12. Vortex tubes three times 20sec.
13. Centrifuge 2' at 15000rpm.
14. Transfer aqueous phase in tubes containing 30µl of 3M Na Ac pH 5.3 (autoclaved).
15. Add 600µl Ethanol absolute.
16. Incubate one hour at -20°C.
17. Centrifuge 15min at 15000rpm at 4°C.
18. Dry pellets and resuspend the three pellets in the same 100µl of bidistilled autoclaved water (Sigma W4502).
19. Carefully quantify RNA and use 100µg for RNA clean up.
RNA clean up:
1. The RNA clean up is an essential step for the quality of the Reverse Transcription. Use a Rneasy minikit (Qiagen, ref : 74106) for RNA clean up. Just follow the recommendations of Qiagen.
2. Elute the column with 50µl of water a first time, then re-elute a second time with the same 50µl.
3. Quantify your purified RNA. You will need 20µg for cDNA synthesis.

tag: Wild-type, ura-, G418, no drug mat a

source_name: Sce16, reference

growth_protocol: No drug control


title: Upper respiratory tract infection (Viro3P11-020)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-019)

description: probe 70 oligo


title: Pneumonia (Viro3P10-257)

description: RdABC amplified RNA from Nasal Lavage

tag: Pneumonia


title: No respiratory symptoms (Viro3P10-259)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-255)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-013)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-041)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-258)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-014)

description: probe 70 oligo


title: Upper respiratory tract infection (Viro3P11-011)

description: probe 70 oligo


title: Upper respiratory tract infection (Viro3P10-250)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P10-252)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-251)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-248)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-237)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-239)

description: probe 70 oligo


title: No respiratory symptoms (Viro3P10-245)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-242)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-231)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-227)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-244)

description: probe 70 oligo


title: Upper respiratory tract infection (Viro3P10-246)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-247)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P10-230)

description: RdABC amplified RNA from Nasal Lavage

tag: Asthma


title: Bronchiolitis (Viro3P10-232)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-225)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-243)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-241)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-226)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-229)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-236)

description: probe 70 oligo


title: Pneumonia (Viro3P10-228)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-240)

description: probe 70 oligo


title: Asthma (Viro3P10-223)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-222)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-199)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-198)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-147)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-148)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-144)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P10-200)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-197)

description: RdABC amplified RNA from Nasal Lavage


title: Planktonic growth, 13503929

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae serotype 1 strain s4074 RNA extracted after growth in cell-free DMEM broth or after planktonic growth over a monolayer of SJPL cells.

scan_protocol: Arrays were scanned with a  Perkins Elmer ScanArray, and data was acquired using SpotFinder v3.1.1.

data_processing:
NORMALIZATION WITH MIDAS :
- One Bad Channel Tolerance Policy parameter on how to deal with one-bad-channel spots = Generous
- Net intensities were normalized using Lowess algorithm (MIDAS).  Mode = block, smoothing parameter = 0.33, reference = Cy3
- In slide replicate analysis to merge data with same unique identifier

organism: Actinobacillus pleuropneumoniae

label_protocol:
RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and amino-allyl dUTP. Samples were then indirectly labelled with Cy3 or Cy5 esters. Complete protocol is described in :
Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

extract_protocol: Monolayers of SJPL cells in T175 flasks were infected for 3h with 100 ul of an OD600 of 0.6 culture of A. pleuropneumoniae (MOI of 10:1).  Planktonic bacteria were harvested in the culture supernatant while adherent bacteria were harvested with the epithelial cells in PBS buffer.  Ice cold RNA degradation stop solution (95% ethanol, 5% buffer-saturated phenol) was added to all samples at a 1:10 (v/v) ratio, and samples were then frozen at -80ºC after a 5 min centrifugation at 4000 g. The isolation of bacterial RNA was carried out using the QIAGEN RNeasy MiniKit with an in-column DNAse treatment, as prescribed by the manufacturer.  RNA was further treated with Ambion’s Turbo DNase to ensure that contaminant DNA was eliminated from the samples.

tag: serotype 1, strain s4074

tag: planktonic bacteria living over SJPL cells

tag: grown in DMEM


title: Upper respiratory tract infection (Viro3P10-009)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (VIro3P10-254)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-008)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P10-146)

description: RdABC amplified RNA from Nasal Lavage


title: Sante_30m_3_virus_vs_mock

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: Biological replicate 3 of 3.

hyb_protocol: cDNA synthesis and hybridization was carried out using 3DNA Array 900 kit (Genisphere)

scan_protocol: Microarrays were scanned using a LS200 scanner (TECAN)

data_processing: The TIFF images were quantified using ArrayPro® Analyzer 4.5 software (Media Cybernetics, USA). Quality control was performed and low quality spots: (i) non-uniform spots (mean (signal) / SD (signal) < 1), (ii) spots with low signal/background ratio (mean (signal) / mean (background) < 1.5) or (iii) spots with low signal to noise ratio (SNR) < 3 were downweighted. Additionally empty or non-validated spots were downweighted (weight flag =0). Data analysis was done in R computing environment (http://www.R-project.org). Background was measured locally. For both channels, signal (trimmed mean of the whole variable spot area) and background (trimmed mean of the spot’s local corners) intensities were calculated. Background was subtracted using the option half. Data was then normalized using loess normalization.

organism: Solanum tuberosum

source_name: cv. Sante, mock - inoculated leaves, 12hpi

growth_protocol: Grown in soil in growth chamber using 16 h period of light (21±2 °C) and 8 h of darkness (18±1 °C), light intensity 70-90 mmol m-2 s-2 , 75±2 % humidity

extract_protocol: Total RNA  was isolated by RNeasy Plant Mini kit (Qiagen), treated with DNAse and purified and concentrated with RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Carborundum-dusted leaves rubbed with sap of healthy or virus infected plant. Samples (pooled inoculated leaves) collected 0.5 and12 hours post inoculation

tag: cultivar

value: Sante

tag: treatment

value: mock inoculation

tag: time

value: 30 minutes after inoculation

tag: pooled leaf material from 6-8 plants, 2-3 leaves er plant

source_name: cv. Igor, virus - inoculated leaves, 12hpi

value: virus inoculation

tag: pooled leaf material from 6-8 plants, 2-3 leaves per plant


title: Planktonic growth, 13503930

hyb_protocol: Complete protocol is described in : Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.


title: Pneumonia (Viro3P10-080)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-041)

description: RdABC amplified RNA from Nasal Lavage


title: Sante_12h_3_virus_vs_mock

description: Biological replicate 3 of 3.

source_name: cv. Sante, virus - inoculated leaves, 12hpi

label_protocol: cDNA synthesis and hybridization was carried out using 3DNA Array 900 kit (Genisphere)

value: 12h after inoculation

source_name: cv. Igor, mock - inoculated leaves, 12hpi


title: Upper respiratory tract infection (Viro3P10-006)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-145)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P10-010)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P10-042)

description: RdABC amplified RNA from Nasal Lavage


title: Planktonic growth, 13503932


title: Pneumonia (Viro3P10-007)

description: RdABC amplified RNA from Nasal Lavage


title: Sante_30m_1_virus_vs_mock

description: Biological replicate 1 of 3.


title: Sante_30m_2_virus_vs_mock

description: Biological replicate 2 of 3.


title: Planktonic growth, 13503928


title: Adherent growth, 13303308

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae serotype 1 strain s4074 RNA extracted after growth in cell-free DMEM broth or after adhesion to a monlayer of SJPL cells.

tag: bacteria that adhered to SJPL cells

extract_protocol: Monolayers of SJPL cells in T175 flasks were infected for 3h with 100 ul of an OD600 of 0.6 culture of A. pleuropneumoniae (MOI of 10:1).  Planktonic bacteria were harvested in the culture supernatant while adherent bacteria were harvested with the epithelial cells in PBS buffer.  Ice cold RNA degradation stop solution (95% ethanol, 5% buffer-saturated phenol) was added to all samples at a 1:10 (v/v) ratio, and samples were then frozen at -80ºC after a 5 min centrifugation at 4000 g. The isolation of bacterial RNA was carried out using the QIAGEN RNeasy MiniKit with an in-column DNAse treatment, as prescribed by the manufacturer.  RNA was further treated with Ambion’s Turbo DNase to ensure that contaminant DNA was eliminated from the samples


title: Adherent growth, 13303302


title: Igor_30m_1_virus_vs_mock

description: Biological replicate 1 of 3.

value: Igor


title: Bronchiolitis (Viro3P10-005)

description: RdABC amplified RNA from Nasal Lavage


title: Adherent growth, 13303931

tag: serotype 1, strain S4074


title: Igor_30m_2_virus_vs_mock

description: Biological replicate 2 of 3.


title: Igor_12h_4_virus_vs_mock

description: Biological replicate 4 of 4.


title: Igor_12h_2_virus_vs_mock

description: Biological replicate 2 of 4.


title: Adherent growth, 13303306


title: Igor_12h_1_virus_vs_mock

description: Biological replicate 1 of 4.


title: No respiratory symptoms (Viro3P10-001)

description: RdABC amplified RNA from Nasal Lavage


title: Igor_30m_3_virus_vs_mock

description: Biological replicate 3 of 3.


title: Upper respiratory tract infection (Viro3P10-002)

description: RdABC amplified RNA from Nasal Lavage


title: Igor_12h_3_virus_vs_mock

description: Biological replicate 3 of 4.


title: No respiratory symptoms (Viro3P10-004)

description: RdABC amplified RNA from Nasal Lavage


title: Sante_12h_2_virus_vs_mock

description: Biological replicate 2 of 3.


title: Sante_12h_1_virus_vs_mock

description: Biological replicate 1 of 3.


title: RT4D6_wild type Sox10 siRNA_rep1

status: Public on Jul 08 2008

city: Seoul

first: Sanghyuk

last: Lee

address: 11-1 Daehyun-dong, Seodaemun-gu

department: Division of Life and Pharmaceutical Sciences

country: South Korea

institute: Ewha Womans University

description: standard Affymetrix protocol

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

label: Biotin

organism: Rattus norvegicus

source_name: RT4D6 Schwannoma cells, treated with wild type siRNA for Sox 10, 48 hours

label_protocol: Protocol from BioArray High Yield RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY

extract_protocol: Qiagen protocol

tag: Rat Schwannoma cell line that express genes associated with glial characteristics including Sox10, p75, GFAP, and S100.  For additional information please see

value: Hai, M., Muja, N., DeVries, G.H., Quarles, R.H. and Patel, P.I.

tag: (2002) Comparative analysis of Schwann cell lines as model systems for myelin gene transcription studies. J Neurosci Res 69:497–.508.


title: RT4D6_mutant Sox10 siRNA_rep2

description: standard Affymetrix protocol

source_name: RT4D6 Schwannoma cells, treated with mutant siRNA for Sox 10, 48 hours


title: Serous ovarian carcinoma sample, stage IV, grade 2 (T6126)

type: genomic

city: Amsterdam

first: Marlies

last: Nowee

state: Noord-Holland

address: Van der Boechorststraat 7

department: Department of Obstetrics and Gynaecology

country: Netherlands

institute: VU University Medical Center

description: no additional information

hyb_protocol: The test and reference DNAs together with 100 ug human Cot-1 DNA were hybridized to the BAC arrays for ~48 hrs at 37C. After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 uM DAPI and sealed with a cover slip.

scan_protocol: A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998). Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).

data_processing: The log2ratio of the total integrated Cy3 and Cy5 intensities for each spot after background subtraction was calculated, normalized to the median log2ratio of all the clones on the array and the average of the triplicates calculated using a second custom program, SPROC. Automatic data filtering to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 within each segmented spot and low reference/DAPI signal intensity was also carried out using SPROC. Data files were subsequently manually edited by rejecting clones for which only one spot of the triplicate survived after SPROC analysis and for which the standard deviation of the log2ratio of the triplicate was >0.2. For each tumor, the data are plotted as the mean log2ratio of the triplicate spots for each clone normalized to the genome median log2ratio. The clones are ordered by position in the genome (UCSC draft genome sequence, August 2001 freeze) beginning at 1p and ending with Xq.

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA from microdissected paraffin embedded serous ovarian carcinoma labeled with Cyanine-3

label_protocol: The tumor genomic DNA and normal female reference DNA (300 ng each) were labeled by random priming in separate 50 ul reactions to incorporate Cy3 and Cy5, respectively.

extract_protocol: Tumor DNAs were extracted from 20 microdissected consecutive 10 µm buffered, formalin-fixed paraffin embedded sections using a QIAamp DNA mini kit following a modification of the manufacturer’s protocol (Weiss et al., 1999).

tag: DNA isolated from paraffin embedded ovarian carcinoma

source_name: normal female genomic DNA

extract_protocol:
Microarray Core UCSF Comprehensive Cancer Center
Standard Operating Procedure
Title: DNA Isolation from Whole Blood
SOP No.: MC 019 Version: 4 Date: 3-9-04
Authors: R. Segraves Reviewed: R. Davis
1.0 Materials
1. Approximately 0.5 to1 liter each of Human QNS (Quantity Not Sufficient) male and female blood.
2. 50 mL polypropylene centrifuge tubes with screw on or snap caps.
3. Access to a BSL-2 level area with appropriate safeguards and hood.
4. Serological pipets in 5mL, 25mL, and 50mL sizes and an automated pipet controller.
5. Centrifuge set for 50mL tubes.
6. Erythrocyte Lysis buffer; 9 volumes of 0.155 M NH4Cl (MW 53.49 X 0.155 = 8.291 grams into 1 Liter) and 1 volume of 0.17 M Tris, set to a pH of 7.65. This solution should be measured precisely.
7. Wash Buffer; 10 mM NaCl (5 mL of 1.0M NaCl into 495 mL dH2O) and 10 mM EDTA (10 mL of 0.5M EDTA into 490 mL dH2O).
8. Nuclei Lysis Buffer; 400 mM NaCl, 10 mM Tris, 2 mM EDTA, pH 8.2.
9. Protease K 500 ug
10. 20% SDS solution.
11. Saturated NaCl solution at approximately 6 M.
12. Ice cold 100% EtOH
13. Ice cold 70% EtOH.
14. 1.5 mL Eppendorf tubes
15. Fluorometer and cuvettes
2.0 Procedure for Isolation of DNA from Human Blood
1. If desired, combine partial bags of male blood into one bag. If reference DNA from a single donor is desired keep individual bags separate. Repeat with female blood and place back into refrigerator. The following steps should be performed on only male blood until complete, then with female blood to prevent inadvertent cross-contamination.
2. Place approximately 50 mL aliquots of the male blood into clean 50 mL tubes.
3. Centrifuge the blood at 4,000 rpm at 4°C for 10 minutes.
4. The blood will separate into serum and solids. Aspirate off and discard the top layer of serum.
5. Using a 10 mL serological pipet, remove the top 1/4-inch of red blood cells from the remaining dark brown blood and place this into new 50 mL centrifuge tubes. This layer is called the buffy coat and this is where most white blood cells will be found. Discard the remaining red blood cells. Combine the buffy coats from 2-3 tubes to a volume of approximately 10 mL.
6. Combine the approximately 10 mL of red and white blood cell mix with 3-5 volumes (fill the 50 mL tube to the top with Lysis Buffer) of Erythrocyte Lysis Buffer preheated to 37 °C. This should lyse the red blood cells and hopefully not the white blood cells. Incubate for 5 minutes at 37°C.
7. Centrifuge the lysate for 10 minutes at 4,000 rpm at 4°C.
8. Remove all but 4-5 mL of the supernatant above the loose dark brown pellet that contains the white blood cells.
9. Add 25 mL of the wash solution (NaCl and EDTA) and resuspend the pellet by vigorously shaking with the lid on tight. Centrifuge again at 4,000 rpm and 4°C for 10 minutes. Aspirate off all but 4-5 mL of wash solution above the pellet.
10. Repeat step 9. Repeat the wash step until the pellet has turned white.
11. Resuspend the pellet in 10 mL of Nuclei Lysis Buffer. Be sure the pellet is broken up so that the SDS and Protease K can get to the cells.
12. Add 330 ìL of 20% SDS solution and 500 ìg of Protease K (resuspended at 20 ug/uL for a total of 25 uL) and vortex to mix well. The combination of nuclei lysis buffer and SDS and Protease K should lyse the outer cell membrane and the internal nuclear membrane and free the white blood cell DNA to solution.
13. Incubate at 37°C overnight or until the solution is clear.
14. Add 3.3 mL of supersaturated NaCl (6 M) to the clear solution. Vortex for 15 seconds. This “salting out” step precipitates proteins and leaves DNA in solution.
15. Centrifuge at 4,000 rpm at 4°C for 10 minutes. Transfer supernatant to a new 50 mL tube. The supernatant may look like an opaque, viscous blob (like snot) with a yellowish tinge at the bottom. It can be hard to work with.
16. Add 25 mL x 100% EtOH to the tube and invert the tube several times to mix well. The DNA should readily precipitate out from solution and float to the surface, if it hasn’t already done so.
17. Spool the floating DNA blob into a new 1.5 mL Centrifuge tube. Fill the tube with 70% EtOH and vortex for 1 minute.
18. Let stand for 15 minutes. Pour out EtOH and wipe excess EtOH out of the tube with a rolled chem-wipe.
19. Air dry the DNA for 10 - 20 minutes to insure all excess EtOH has evaporated.
20. Resuspend the pellet in dH2O. (see note 1.)
21. Using a 1000 ìL pipet followed by a 200 ìL pipet, pipet the liquid up and down to shear the DNA and to make the solutions less viscous.
22. Using a Fluorometer, determine DNA concentration. Aliquot DNA into new 1.5 mL tubes and dilute to a concentration of 600 ng/ ìL (0.6 ìg/ ìL). Label and store aliquots at -20°C.
3.0 Notes
1. Tris/EDTA is sometimes used to resuspend the DNA. It may take an hour or two to fully resuspend the DNA.
4.0 Acknowledgements
1. S.A.Miller, D.D.Dykes, and H.F.Polesky: A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 16, 1215, 1988.
2. Linda Madisen, David I. Hoar, Catherine D. Holroyd, Margaret Crisp, and M.E. Hodes: DNA Banking: The effects of storage blodd and isolated DNA on the integrity of DNA. American Journal of Medical Genetics 27, 379-390, 1987.

tag: Genomic DNA isolated from human blood


title: Non-islet pancreatic cells 2

city: Cambridge

first: qiao

last: zhou

state: MA

address: 7 Divinity Ave

department: Stem cell and regenerative biology

institute: Harvard University

description: pancreatic tissue after islets were removed from pdxa-gfp animal

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: with Beadstudio, standardized.  Differentially expressed genes identified with illumina recommended parameters: pvalue<0.05, diff score >30, average signal >100

label: biotin

organism: Mus musculus

source_name: non-islet pancreatic cells

label_protocol: Total prep RNA amplification kit (Ambion)

extract_protocol: ~5000 GFP+ cells, 4-5 islets, or ~10,000 no islet cells per sample was extracted for total RNA with trizol reagent (invitorgen)

tag: adult mouse pdx1-GFP


title: Non-islet pancreatic cells 3


title: RT4D6_mutant Sox10 siRNA_rep1

description: standard Affymetrix protocol


title: Pneumonia (Viro3P11-017)

description: probe 70 oligo

tag: Pneumonia


title: Non-islet pancreatic cells 1


title: yeast_on_acetate_CO_24hr

city: Seattle

first: Kin

last: Chan

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: This array is one of a series of arrays of yeast whose cell divisions are reversibly arrested when made anoxic on solid acetate media, using either pure nitrogen or pure carbon monoxide.

hyb_protocol: Dissolved 15g powdered non-fat milk in 370mL water, 120mL 20x SSC, 5mL 10% SDS.  Warmed solution in 42 degree water bath for ~45 minutes.  Put slides into solution and incubated for 1 hour at 42 degrees.  Washed slides vigorously in water, then in 100% 2-propanol.  Dried slides by spinning at 500xg for 5 minutes.  aRNA samples were thawed.  10% SDS and 20x SSC were added to attain final concentrations of 0.2% SDS in 3x SSC.  Heated samples at 99 degrees for 5 minutes.  Recollected samples by centrifugation.  Added sample onto array area of slides and covered with coverslip.  Incubated slides ~16 hours in sealed hybridization chamber at 63 degrees.  After hybridization, washed slides in 1x SSC/ 0.03% SDS.  Coverslips were separated from slides by gentle agitation during washing.  Then washed slides in 1x SSC.  Soaked slides in 0.2x SSC while shaking at 60 RPM in the dark for 20 minutes.  Soaked slides in 0.05x SSC while shaking at 60 RPM in the dark for 20 minutes.  Dried slides by gentle centrifugation for 5 minutes.

scan_protocol: Arrays were scanned using an Axon Instruments GenePix4000B scanner at 635 and 532 nm with 10 micron resolution.  PMT settings for wavelengths were adjusted and balanced using GenePix Pro 6.0 software.

data_processing: Image files were loaded onto GenePix Pro 6.0 software.  Auto-alignment was applied.  Bad spots were flagged.  Locations of misaligned spots were corrected.  Images were then analyzed to generate .gpr files.  .gpr files were filtered using GDFilter, a program developed at FHCRC to remove data from spots < 75 microns in diameter or signal-to-noise ratios < 3.  Data were loaded onto a GeneTraffic server.  The “Lowess (Sub-Grid, non-flagged)” normalization was applied.  Data was then exported using GTExport, another application developed at FHCRC.

source_name: yeast on acetate, exposed 24 hr to CO

label_protocol: Diluted 4.0 ug aRNA in 4.5 uL water.  Added 4.5 uL 0.2M sodium bicarbonate.  Vortexed and collected by centrifugation.  Added 5.5 uL of dye.  Vortexed and collected by centrifugation.  Incubated at room temperature for 1 hour in the dark.

extract_protocol: RNA extractions were initiated by resuspending each pellet in 400 uL TES (10 mM Tris-HCl, pH 7.5, 10 mM EDTA, 0.5% SDS) and 400 uL acid phenol (pre-warmed to 65 degrees) with vigorous vortexing. Cells were incubated at 65 degrees for 1 hour, with vortexing every 10 minutes. Suspensions were transferred to microfuge tubes and put on ice for 5 minutes, then centrifuged at top speed for 10 minutes at 4 degrees on an Eppendorf Minispin centrifuge. Aqueous phases were transferred to fresh tubes and extracted with 400 uL room temperature acid phenol twice more, followed by a single extraction with 400 uL chloroform. RNA was then precipitated from the aqueous phase using 40 uL 3M sodium acetate, pH 5.3 and 1 uL ice-cold ethanol, and centrifuged for 20 minutes. Pellets were washed with 0.5 mL ice-cold 80% ethanol and centrifuged for 5 minutes. RNA was redissolved in 20 uL water.

tag: strain

tag: media

value: solid YP acetate

tag: pre-grown overnight in liquid YPD

source_name: yeast on acetate, exposed 24 hr to air


title: Serous ovarian carcinoma sample, stage III, grade 3 (T5614)

description: no additional information


title: yeast_on_acetate_N2_24hr

source_name: yeast on acetate, exposed 24 hr to N2


title: Serous ovarian carcinoma sample, stage IV, grade 2 (T8131)

description: no additional information


title: Serous ovarian carcinoma sample, stage IV, grade 2 (T15783)

description: no additional information


title: E.coli W3110, 45 minutes after oxygen downshift, sample S3

city: Oulu

first: Jaakko

last: Soini

address: Erkki Koiso-Kanttilan katu 1

department: Process and Environmental Engineering

country: Finland

institute: University of Oulu

description: In the oxygen downshift experiment the aim was to study the gene expression profiles in connection to downshift of oxygen supply by step decrease of agitation rate and air supply. E. coli W3110 strain cultivated in 8L fed-batch fermentation and the S3 sample was taken under oxygen limitation 45 min after the oxygen downshift.

data_processing: GCOS 1.0

organism: Escherichia coli

source_name: E.coli W3110, fermentation sample taken 45 minutes after oxygen downshift

label_protocol: According to Affymetrix E.coli Genome 2.0 array instructions. Genechip DNA labeling reagent.

growth_protocol:
The cultivations were performed in a Biostat C 15 L bioreactor with the DCU-3 controlling unit and MFCS-win supervisory system (Sartorius) with an initial working volume of 8 L. The mineral salt medium contained per liter: 14.6 g K2HPO4, 3.6 g NaH2PO4 × 2 H2O, 2.0 g Na2SO4, 2.47 g (NH4)2SO4, 0.5 g NH4Cl, 1.0 g (NH4)2-H-citrate, 2 mM MgSO4, 0.1 g thiamine hydrochloride, 0.1 mL antifoam 204 (Sigma) and 2 mL trace element solution (1). The initial glucose concentration was 40 g L-1. The feed solution contained 650 g L-1 glucose. 2 mL L-1 of sterile filtered 1M MgSO4 were added regularly per OD600=10 increase.
Two precultures were performed in LB medium and mineral salt medium with 10 g L 1 of glucose without antifoam agent consecutively at 37 °C at a rotary shaker at 180 rpm. Main cultivations were started as batch cultures at a temperature of 37 °C. The pH was kept at 7.0 by controlled addition of 25% ammonia solution. At the end of the exponential growth phase (cell dry weight about 16 g L-1) the stirrer rate was lowered from 1000 rpm to 500 rpm, to provoke oxygen limitation by decreased oxygen transfer. Constant glucose feed of 100 g L-1 h-1 was started 15 min after the oxygen drop which was enough to ensure glucose excess during the whole cultivation.
References:
1.Holme T, Arvidson S, Lindholm B, and Pavlu B. 1970. Enzymes: Laboratory-scale production. Process Biochemistry 62-66.

extract_protocol:
Samples for microarray analysis were collected as described earlier [1], (Samples were shortly mixed by vortexing, divided in 0.5 mL aliquots and 1. centrifuged for 3 min at 16,100 ×g and +4 °C. The pellets were resuspended in 250 µL of RNALater (Ambion, USA) and stored at -20 °C until analysis. RNA was extracted using the total RNA kit (A&A Biotechnology, Poland) .
References
1.	Neubauer, A., J. Soini, M. Bollok, M. Zenker, J. Sandqvist, J. Myllyharju, and P. Neubauer. 2007. Fermentation process for tetrameric human collagen prolyl 4-hydroxylase in Escherichia coli: improvement by gene optimisation of the PDI/beta subunit and repeated addition of the inducer anhydrotetracycline. J Biotechnol 128:308-321.

tag: Strain

value: Escherichia coli W3110 [F– IN(rrnD-rrnE)1]


title: RT4D6_wild type Sox10 siRNA_rep2

description: standard Affymetrix protocol


title: Serous ovarian carcinoma sample, stage III, grade 2 (T13700)

description: no additional information


title: E.coli W3110, 75 minutes after oxygen downshift, sample S4

description: In the oxygen downshift experiment the aim was to study the gene expression profiles in connection to downshift of oxygen supply by step decrease of agitation rate and air supply. E. coli W3110 strain cultivated in 8L fed-batch fermentation and the S4 sample was taken under oxygen limitation 75 min after the oxygen downshift.

hyb_protocol: According to Affymetrix E.coli Genome 2.0 array instructions

source_name: E.coli W3110, fermentation sample taken 75 minutes after oxygen downshift


title: Whole islet 2

description: iselts hand picked from adult pdx-gfp transgenic animals

source_name: whole islet


title: Induced beta cells 2

description: rag-/- adult pancreas infected with M3 adeno virus 1 month FACS sorted contain 22% ins+ cells

source_name: induced beta cells

tag: adult mouse GFP+


title: Serous ovarian carcinoma sample, stage III, grade 2 (T0311)

description: no additional information


title: E.coli W3110, 15 minutes after oxygen downshift, sample S2

description: In the oxygen downshift experiment the aim was to study the gene expression profiles in connection to downshift of oxygen supply by step decrease of agitation rate and air supply. E. coli W3110 strain cultivated in 8L fed-batch fermentation and the S2 sample was taken under oxygen limitation 15 min after the oxygen downshift.

scan_protocol: According to Affymetrix E.coli Genome 2.0 array instructions

source_name: E.coli W3110, fermentation sample taken 15 minutes after oxygen downshift


title: Whole islet 1


title: Induced beta cells 1


title: Serous ovarian carcinoma sample, stage III, grade 3 (T6976)

description: no additional information


title: yeast_on_acetate_CO_120min

source_name: yeast on acetate, exposed 120 min to CO

source_name: yeast on acetate, exposed 120 min to air


title: yeast_on_acetate_N2_120min

source_name: yeast on acetate, exposed 120 min to N2


title: E.coli W3110, 15 minutes before oxygen downshift, sample S1

description: In the oxygen downshift experiment the aim was to study the gene expression profiles in connection to downshift of oxygen supply by step decrease of agitation rate and air supply. E. coli W3110 strain cultivated in 8L fed-batch fermentation and the S1 sample was taken under aerobic conditions 15 min before the oxygen downshift.

source_name: E.coli W3110, fermentation sample taken 15 minutes before oxygen downshift

extract_protocol:
Samples for microarray analysis were collected as described earlier [1], (Samples were shortly mixed by vortexing, divided in 0.5 mL aliquots and 1. centrifuged for 3 min at 16,100 ×g and +4 °C. The pellets were resuspended in 250 µL of RNALater (Ambion, USA) and stored at -20 °C until analysis. RNA was extracted using the total RNA kit (A&A Biotechnology, Poland) .
References
1. Neubauer, A., J. Soini, M. Bollok, M. Zenker, J. Sandqvist, J. Myllyharju, and P. Neubauer. 2007. Fermentation process for tetrameric human collagen prolyl 4-hydroxylase in Escherichia coli: improvement by gene optimisation of the PDI/beta subunit and repeated addition of the inducer anhydrotetracycline. J Biotechnol 128:308-321.


title: Induced beta cells 3


title: Whole islet 3


title: Serous ovarian carcinoma sample, stage III, grade 3 (T154)

description: no additional information


title: Serous ovarian carcinoma sample, stage III, grade 2 (T15990)

description: no additional information


title: yeast_on_acetate_N2_60min

source_name: yeast on acetate, exposed 60 min to N2

source_name: yeast on acetate, exposed 60 min to air


title: yeast_on_acetate_CO_60min

source_name: yeast on acetate, exposed 60 min to CO


title: Serous ovarian carcinoma sample, stage III, grade 2 (T10256)

description: no additional information

source_name: Genomic DNA from microdissected paraffin embedded serous ovarian carcinoma labeled with Cyanine-3

source_name: normal female genomic DNA


title: yeast_on_acetate_CO_45min

source_name: yeast on acetate, exposed 45 min to CO

source_name: yeast on acetate, exposed 45 min to air


title: Serous ovarian carcinoma sample, stage II, grade 1 (T5843)

description: no additional information


title: Serous ovarian carcinoma sample, stage III, grade 2 (T5400)

description: no additional information


title: Serous ovarian carcinoma sample, stage III, grade 3 (T11262)

description: no additional information


title: yeast_on_acetate_N2_45min

source_name: yeast on acetate, exposed 45 min to N2


title: yeast_on_acetate_N2_15min

source_name: yeast on acetate, exposed 15 min to N2

source_name: yeast on acetate, exposed 15 min to air


title: yeast_on_acetate_N2_30min

source_name: yeast on acetate, exposed 30 min to N2

source_name: yeast on acetate, exposed 30 min to air


title: yeast_on_acetate_CO_15min

source_name: yeast on acetate, exposed 15 min to CO


title: Serous ovarian carcinoma sample, stage I, grade 3 (T5730)

description: no additional information


title: yeast_on_acetate_CO_30min

source_name: yeast on acetate, exposed 30 min to CO


title: DBA/2 iron-enriched (DBAWT57)

status: Public on Jul 07 2008

city: Toulouse

first: Marie-Paule

last: Roth

address: Chu Purpan

country: France

institute: Inserm

description: Information from probe features was extracted from microarray scan images using the Agilent Feature Extraction software v.9.5.1.

hyb_protocol: Agilent's standard protocol

scan_protocol: Agilent's scanner

data_processing: As recommended by the manufacturer

source_name: liver

label_protocol: Agilent's Low RNA Input Linear Amplification Kit PLUS (One-color)

extract_protocol: RNeasy Lipid Tissue Kit (Qiagen)

tag: age:7 weeks

tag: diet

value: iron-enriched (8.3 g iron/kg)


title: DBA/2 iron-deficient (DBAWT61)

value: iron-deficient (<3 mg iron/kg)


title: Serous Fallopian tube carcinoma sample, stage III, grade 2 (T10134)

description: no additional information

source_name: Genomic DNA from microdissected paraffin embedded serous Fallopian tube carcinoma labeled with Cyanine-3

tag: DNA isolated from paraffin embedded Fallopian tube carcinoma


title: DBA/2 iron-enriched (DBAWT56)


title: DBA/2 iron-enriched (DBAWT55)


title: DBA/2 iron-deficient (DBAWT62)


title: DBA/2 iron-deficient (DBAWT60)


title: DBA/2 iron-balanced (DBAWT52)

value: iron-balanced(200mg iron/kg)


title: DBA/2 iron-deficient (DBAWT58)


title: DBA/2 iron-enriched (DBAWT54)


title: DBA/2 iron-balanced (DBAWT51)


title: DBA/2 iron-enriched (DBAWT53)


title: DBA/2 iron-balanced (DBAWT49)


title: DBA/2 iron-balanced (DBAWT50)


title: DBA/2 iron-balanced (DBAWT48)


title: C57BL/6 iron-deficient (C57WT56)


title: C57BL/6 iron-deficient (C57WT57)


title: C57BL/6 iron-enriched (C57WT52)

value: iron-enriched(8.3 g iron/kg)


title: DBA/2 iron-deficient (DBAWT59)


title: C57BL/6 iron-enriched (C57WT48)


title: C57BL/6 iron-deficient (C57WT53)


title: VEC_positive_confluent_rep2

status: Public on Jul 06 2008

city: Milan

first: Elisabetta

last: Dejana

address: Via Adamello, 16

country: Italy

institute: IFOM-IEO-CAMPUS

description:
Synthesis of biotinylated cRNA targets, array hybridization (GeneChips MG_U74Av2 and MG_U74Bv2), staining and scanning were performed according to the Affymetrix standard protocols, starting from 15 μg of total RNA. Two copies of the GeneChips were hybridized with each cRNA sample.
values, % present calls, average signal value, etc).

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning parameters

data_processing:
The MAS5 algorithm was used to determine the expression levels of mRNAs; the absolute analysis was performed using default parameters and scaling factor 500. Report files were extracted for each chip, and performance of
labelled target was evaluated on the basis of several values (scaling factor, background and noise. Gene expression levels were normalized on the median over all samples. Annotation of Probe Sets is according to Affymetrix Annotation Tables (release May 31, 2007)

source_name: VE-Cadherin positive cells, confluent condition

label_protocol: Standard Affymetrix labeling protocol

extract_protocol: standard guanidinium isothiocyanate lysis buffer and cesium chloride ultracentrifugation.

tag: ECs derived from murine embryonic stem cells with homozygous null mutation of the VE-cadherin gene (VEC null) [Balconi,G., Spagnuolo,R., & Dejana,E. Development of endothelial cell lines from embryonic stem cells

value: A tool for studying genetically manipulated endothelial cells in vitro. Arterioscler.Thromb. Vasc. Biol. 20, 1443-1451 (2000)].

tag: The wild type form of VE-cadherin was introduced in these cells (VEC positive) as described in detail by [Lampugnani,M.G. et al. Contact inhibition of VEGF-induced proliferation requires vascular endothelial cadherin, beta-catenin, and the phosphatase DEP-1/CD148. J. Cell Biol. 161,793-804 (2003).


title: C57BL/6 iron-enriched (C57WT51)


title: C57BL/6 iron-deficient (C57WT54)


title: C57BL/6 iron-balanced (C57WT47)


title: C57BL/6 iron-balanced (C57WT44)


title: VEC_positive_sparse_rep1

source_name: VE-Cadherin positive cells, sparse condition


title: C57BL/6 iron-enriched (C57WT50)


title: VEC_positive_confluent_ChipB_rep2


title: C57BL/6 iron-balanced (C57WT43)


title: C57BL/6 iron-enriched (C57WT49)


title: C57BL/6 iron-balanced (C57WT46)


title: C57BL/6 iron-balanced (C57WT45)


title: VEC_positive_confluent_rep1


title: VEC_positive_sparse_rep2


title: C57BL/6 iron-deficient (C57WT55)


title: VEC_Null_confluent_rep1

source_name: VE-Cadherin negative cells, confluent condition


title: VEC_positive_sparse_ChipB_rep2


title: VEC_Null_sparse_rep2

source_name: VE-Cadherin negative cells, sparse condition


title: VEC_Null_confluent_rep2


title: VEC_positive_confluent_ChipB_rep1


title: VEC_Null_confluent_ChipB_rep2


title: VEC_positive_sparse_ChipB_rep1


title: VEC_Null_confluent_ChipB_rep1


title: VEC_Null_sparse_rep1

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard Affymetrix scanning parameters

label_protocol: standard Affymetrix labeling protocol


title: VEC_Null_sparse_ChipB_rep1


title: 6780-DOX0.09-rep1

status: Public on Jul 01 2008

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

description: Raw data file is TIGR MEV format

hyb_protocol: See http://microarray.org/sfgf/meebo.do

scan_protocol: See http://microarray.org/sfgf/meebo.do

data_processing: Gridded using TIGR SpotFinder 3.1; normalization done using TIGR MIDAS (http://www.tigr.org TM4 suite). Lowess block normalization (parameter 0.33), stringent checking for background on both channels, standard deviation normalization between and across slides. Spots with SNR>2 and integrated intensity>20000 in both channels selected

source_name: 6780 cell line, 0.09 ng/ml dox treatment

label_protocol: See http://microarray.org/sfgf/meebo.do

growth_protocol: 6780 MYC dependent T-cell lymphoma generated from Emu-SrAlpha (Tet) transgenic mice. CD4/CD8 expressing tumor cells were grown in RPMI medium

extract_protocol: See http://microarray.org/sfgf/meebo.do

tag: tumor cell line

source_name: Stratagene reference RNA

tag: mouse total RNA


title: 6780-DOX20-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 20 ng/ml dox treatment


title: AdHBx transduced UV treated HepG2 cells

city: Singapore

first: Wah Heng

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: HepG2 cells transduced with HBX expressing recombinant Adenoviruses (AdHBx) and treated with UV

hyb_protocol: Hybridization was performed by Nimblegen

scan_protocol: Scanned by Nimblegen Images were quantified by Nimblegen

data_processing: Data normalization done by Nimblegen

source_name: Crosslinked sonicated chromatin fragments from AdHBx transduced HepG2 cells, UV treated immunoprecipitated with anti-HBx antibodies

label_protocol: The ChIP-DNA and Input-DNA were end-labeled with Cy5 and Cy3, respectively, and co-hybridized to a Nimblegen ChIP-chip promoter tiling array (NimbleGen Systems, Inc). The labeling and hybridization was performed by Nimblegen.

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% FCS, 8-16J/m2 UV treatment

extract_protocol: The Chromatin Immunoprecipitation (ChIP) Assay Kit (Upstate Cell Signaling Solutions / Millipore, USA) was employed to isolate Input DNA and ChIP-DNA from chromatin that has been immunoprecipitated with anti-HBx antibodies.

source_name: Input DNA that has been crosslinked but NOT immunoprecipitation with HBx and reverse crosslinked

tag: DNA (Input-DNA) extracted from the total lysate that has been crosslinked (but not immunoprecipitated) and reverse-crosslinked was utilized to normalize for differences in the amount of DNA present in the different samples


title: VEC_Null_sparse_ChipB_rep2


title: LZM3 vs. LZM3000 3 uM zince Replicate 1

status: Public on Jul 04 2008

city: Madison

first: CHANG-YI

last: WU

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: UW-Madison

description: Biological replicate 1 of 2.

hyb_protocol: The cDNA-labeled probes were then hybridized onto an arrayed slide. After hybridization, slides were washed sequential.

scan_protocol: Fluorescence was captured with a GEN III dual-laser confocal scanner (Molecular Dynamics). Fluorescent intensities were quantified using Arrayvision 6.0 (Imaging Research).

data_processing: The ratios of signal intensities (Cy5/Cy3) were normalized by the median output signal intensity for all genes. To remove intensity-dependent measurement artifacts, we normalized the log Cy3/Cy5 fold changes within each microarray slide using the locally weighted scatterplot smoothing (LOWESS) algorithm.

molecule: polyA RNA

label_protocol: mRNA (1.2 µg) was used to generate cDNA probes by reverse transcription (Superscript II, GIBCO) with incorporation of Cy3-dCTP or Cy5-dCTP (Amersham Biosciences).

growth_protocol: LZM + 3uM zinc

extract_protocol: Total RNA was extracted with hot phenol and mRNA was isolated from total RNA using the PolyATtract mRNA Isolation System IV kit (Promega).

tag: Mata  ade6 can1 his3 leu2 trp1 ura3

source_name: Dy1457, labeled with Cyanine-3 (green).


title: 6780-DOX0.06-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.06 ng/ml dox treatment


title: LZM3 vs. LZM3000 3 uM zinc Replicate 2

description: Biological replicate 2 of 2.


title: 6780-DOX0.05-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.05 ng/ml dox treatment


title: Zap1TC-allele vs. vector 1 uM zincReplicate 2

description: Biological replicate 2 of 2.

source_name: Dy1457 transformed Zap1TC

growth_protocol: SD galactose +1uM zinc

source_name: Dy1457 transformed vector pYEF2, labeled with Cyanine-3 (green).


title: 6780-DOX0.03-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.03 ng/ml dox treatment


title: 6780-DOX0.02-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.02 ng/ml dox treatment


title: 6780-DOX0.01-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.01 ng/ml dox treatment


title: 6780-DOX0.07-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.07 ng/ml dox treatment


title: 6780-DOX0.08-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.08 ng/ml dox treatment


title: Prdm1ChIP_WholeCellExtract_slide2

status: Public on Jul 03 2008

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

hyb_protocol: Protocol as described in Wardle et al 2006 (Genome Biology 7:R71).

scan_protocol: Slides were scanned using an Agilent scanner. Images were quantified using Agilent Feature Extraction.

data_processing: Data was analysed using ChIP Analytics 1.3.1 with default settings and no blank subtraction. A probe was considered bound when the enrichment ratio for each feature had a p-value of equal to or less than 0.0078 and the value of p[Xbar] which takes into account the enrichment of neighbouring probes was less than or equal to 0.0075.

organism: Danio rerio

source_name: Immunoprecipitated chromatin

growth_protocol: Zebrafish were injected wuth dominant negative Protein kinase A (dnPKA) at the one cell stage. Embryos were grown to 12-14 somite stage.

extract_protocol: Chromatin immunoprecipitation assay

treatment_protocol: A facs cell sorter was used to collect muscle cells using alpha actin gfp trangenes to identify the cells of interest. The slow muscle domain of the alpha actin gfp embryos was increased by the injection of dominant negative Protein kinase A (dnPKA), which acts an enhancer of hh signalling and leads to increased Prdm1 expression.   Triplicates of 4*106 sorted GFP positive cells, from dnPKA injected embryos at 12-14 somites, were used in a ChIP assay to generate the Cy3 (ChIP) and Cy5 (input) labelled probes for hybridisation to the gene arrays.

tag: Muscle cells

source_name: Whole cell extract


title: 6780-DOX0.04-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0.04 ng/ml dox treatment


title: BC6206: Mainz_N0_untreated_frozen _183

city: Leverkusen

first: Mathias

last: Gehrmann

address: Kaiser-Wilhelm-Allee

department: BTS-PT-AS-AT

country: Germany

institute: Bayer Technology Services GmbH

description: Gene expression data from primary breast tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer’s instructions

extract_protocol: Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For all tumors, samples were snap frozen and stored at -80°C. Tumor cell content exceeded 40% in all samples

tag: storage

value: fresh frozen

tag: node

tag: grade

tag: clinic

value: Mainz


title: Zap1TC-allele vs. vector 1uM zinc Replicate 1

description: Biological replicate 1 of 2.


title: Prdm1ChIP_WholeCellExtract_slide1

label_protocol: Protocol as described in Wardle et al 2006 (Genome Biology 7:R71).


title: 6780-DOX0-rep1

description: Raw data file is TIGR MEV format

source_name: 6780 cell line, 0 ng/ml dox treatment

source_name: Stratagene reference RNA


title: AWBF_invasive_T44B

city: Vancouver

first: Bradley

middle: P

last: Coe

state: BC

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

description: no additional information

hyb_protocol: Hybridizations were performed as described in Coe et al Genes Chromosomes Cancer 2006;45:11-19. Briefly labeled probes were combined in 45ul of DIGEasy based hybridization buffer containing 1100ug Cot-1 DNA, hybridization then took place under a coverslip for 36 hours at 45C. Slides were washed in 0.1X SSC 0.1% SDS 5 x 5 min, and rinsed with 0.1X SSC. Slides were then dried by centrifugation prior to scanning.

scan_protocol: Images were scanned using and API Arrayworx e Auto Scanner. Data was processed using the Softworx (API) analysis package.

data_processing: Data was normalized using the application described in Khojasteh et al BMC Bioinformatics 2005;6:274

source_name: T44B: Lung AWBF - Invasive Area

label_protocol: Genomic DNA was labeled with Cyanine 5 (sample) and Cyanine 3 (reference) using a klenow based random priming procedure as described in Coe et al Genes Chromosomes Cancer 2006;45:11-19.

extract_protocol: Genomic DNA extracted by standard ProtK extraction.

tag: Lung Adenocarcinoma with Bronchioalveolar Features - Invasive Area

source_name: Male Genomic (reference)

label_protocol: see protocol for channel 1

tag: Novagen Male Genomic DNA


title: AWBF_invasive_T6

description: no additional information

source_name: T6: Lung AWBF - Invasive Area


title: AWBF_invasive_T46A

description: no additional information

source_name: T46A: Lung AWBF - Invasive Area


title: AWBF_invasive_T9

description: no additional information

source_name: T9: Lung AWBF - Invasive Area


title: AWBF_invasive_T44A

description: no additional information

source_name: T44A: Lung AWBF - Invasive Area


title: AWBF_invasive_T195

description: no additional information

source_name: T195: Lung AWBF - Invasive Area


title: AWBF_BAC_area_T2

description: no additional information

source_name: T2: T2: Lung AWBF - BAC Area

tag: Lung Adenocarcinoma with Bronchioalveolar Features - BAC Area


title: AWBF_invasive_T43B

description: no additional information

source_name: T43B: Lung AWBF - Invasive Area


title: AWBF_invasive_T19

description: no additional information

source_name: T19: Lung AWBF - Invasive Area


title: AWBF_invasive_T42A

description: no additional information

source_name: T42A: Lung AWBF - Invasive Area


title: AWBF_invasive_T40A

description: no additional information

source_name: T40A: Lung AWBF - Invasive Area


title: AWBF_invasive_T10

description: no additional information

source_name: T10: Lung AWBF - Invasive Area


title: AWBF_invasive_T41B

description: no additional information

source_name: T41B: Lung AWBF - Invasive Area


title: AWBF_invasive_T46B

description: no additional information

source_name: T46B: Lung AWBF - Invasive Area


title: AWBF_BAC_area_T49A

description: no additional information

source_name: T49A: Lung AWBF - BAC Area


title: AWBF_BAC_area_T51A

description: no additional information

source_name: T51A: Lung AWBF - BAC Area


title: AWBF_invasive_T41A

description: no additional information

source_name: T41A: Lung AWBF - Invasive Area


title: AWBF_BAC_area_T30

description: no additional information

source_name: T30: Lung AWBF - BAC Area

source_name: Male Genomic (reference)


title: AWBF_BAC_area_T48A

description: no additional information

source_name: T48A: Lung AWBF - BAC Area


title: AWBF_BAC_area_T5

description: no additional information

source_name: T5: Lung AWBF - BAC Area


title: AWBF_BAC_area_T47A

description: no additional information

source_name: T47A: Lung AWBF - BAC Area


title: AWBF_invasive_T12

description: no additional information

source_name: T12: Lung AWBF - Invasive Area


title: AWBF_BAC_area_T4

description: no additional information

source_name: T4: Lung AWBF - BAC Area


title: AWBF_BAC_area_T3

description: no additional information

source_name: T3: Lung AWBF - BAC Area


title: AWBF_BAC_area_T22

description: no additional information

source_name: T22: Lung AWBF - BAC Area


title: AWBF_BAC_area_T13

description: no additional information

source_name: T13: Lung AWBF - BAC Area


title: mouseTNF_2

first: Li-Fen

address: 299, Campus Dr.

department: Microbiology and Immunology

description:
8-12-week-old NOD.BDC2.5 transgenic mice were injected i.p. with PBS or 3 ug murine TNFalpha; on alternate days for three weeks. At day 24 of treatment, suspensions of LNs and/or splenocytes were stimulated with the indicated concentration of the mimotope (1047-7 peptide (YVAPVWVRME)) at a density of 7-8 x 106 cells/ml, in a final volume of 1 ml in 24-well plates. After prolonged in vitro culture, cells were harvested 12 hrs post transplantation. CD4+ T cells were purified by labeling of monoclonal Abs of surface markers, Vbeta4-FITC and CD4-PE and enriched by Magnetic beads selection followed by FACS sorting. The purity of CD4+ T cells ranged from 95% to 99% depending on individual CD4 T cells preparation. The data in column represents six independent repeated experiments with half of the slides being reverse replicates. We compared RNA from PBE treated group with TNF treated group without including reference RNA.
Simple annotation: TNF, T-cell
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62091.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 5920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jason,,Lih Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.38; Parameter Scan Time = 12:05:55; Parameter PMT Volts = 560; Parameter Scan Date = 2005-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 36386; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.90; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.38; Parameter Scan Time = 12:05:55; Parameter PMT Volts = 600; Parameter Scan Date = 2005-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 109521; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.68; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih

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

source_name: PBS

label_protocol: not provided

extract_protocol: not provided

source_name: TNF


title: AWBF_BAC_area_T1

description: no additional information

source_name: T1: Lung AWBF - BAC Area


title: AWBF_BAC_area_T17

description: no additional information

source_name: T17: Lung AWBF - BAC Area


title: PAO1 treated with azithromycin (2 microgram pr. mL) (replicate B)

status: Public on Mar 26 2008

city: Kgs. Lyngby

first: Mette

middle: E.

last: Skindersoe

address: Matematiktorvet 1. build. 301

country: Denmark

institute: Technical University of Denmark

description: Gene expression data from exponentially growing P. aeruginosa cultures grown in presence of antibiotics

hyb_protocol: Hybridised for 18 h at 55°C to P. aeruginosa genome microarray GeneChip® (Affymetrix).

scan_protocol: The chips were washed and stained according to the Affymetrix protocol.

data_processing: The microarray hybridization signal intensity was scaled to an overall signal average of 2500 using Affymetrix default analysis settings, and present/marginal/absent (based on evaluation of PerfectMatch (PM) and MisMatch (MM) intensities) was evaluated by the use of the Affymetrix GCOS v1.4 software. Only expression value genes estimated being “Present” were included in the further analyses.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 treated with azithromycin (2 microgram pr. mL) (replicate b)

label_protocol: Synthesis of cDNA was performed with 12 microg RNA, 300 ng/microL random primers (Invitrogen™), 1500 U SuperScript III Reverse Transcriptase (Invitrogen™) and 30 U SUPERase۰In™ Rnase Inhibitor (Ambion) according to Affymetrix’s Expression Analysis Protocol. Synthesized cDNA was purified using the QIAquick PCR Purification Kit (QIAGEN) and 3-4 microg cDNA was fragmented using 0.2 U DNase I, FPLC pure™ (Amersham Bioscience) pr. microg cDNA. Fragmented cDNA was terminal labelled with biotin-ddUTP (Enzo Bioarray™ terminal labeling kit).

growth_protocol: ABT medium supplemented with 0.5% cas amino acids were inoculated with exponentially growing P. aeruginosa PAO1 cells to an OD600 of 0.05 and grown at 37°C, 200 rpm in 5 x 500 mL flasks containing 100 mL each.  Samples were retrieved at OD600 2.0

extract_protocol: Samples were retrieved at OD600 2.0, and immediately transferred to two volumes RNAlater (Ambion) and stored at -80°C. RNA was isolated using the “RNeasy Mini Purification Kit” (QIAGEN) according to the provided protocol including the on-column DNase treatment.

treatment_protocol: Exponentially growing cells were added subMIC level antibiotics at OD600 = 0.3


title: Sen_virus_vs_mock_12hpi_2

status: Public on Mar 21 2008

description:
Sen_virus_vs_mock_12hpi_2
Biological replicate 2 of 4.

hyb_protocol: cDNA synthesis and hybridization was carried out using 3DNA Array 900 kit (Genisphere)

scan_protocol: Microarrays were scanned using a LS200 scanner (TECAN)

source_name: cv. Igor, virus - inoculated leaves, 12hpi

extract_protocol: Total RNA was isolated by RNeasy Plant Mini kit (Qiagen), treated with DNAse and purified and concentrated with RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Carborundum-dusted leaves rubbed with sap of healthy or virus infected plant. Samples collected 12 hours post inoculation

tag: cultivar

tag: treatment

tag: time

tag: pooled leaf material from 6-8 plants, 2-3 leaves per plant

source_name: cv. Igor, mock - inoculated leaves, 12hpi


title: PAO1 treated with ciprofloxacin (0.04 microgram pr. mL) (replicate B)

source_name: PAO1 treated with ciprofloxacin (0.04 microgram pr. mL)  (replicate b)


title: PAO1 treated with ceftazidime (0.25 microgram pr. mL) (rep B)

source_name: PAO1 treated with ceftazidime (0.25 microgram pr. mL) (replicate b)


title: MA114: EC-test2-rep 3

status: Public on Jun 21 2008

city: Hong Kong

first: Mary

address: 21 Sassoon Road

department: Dept of Pharmacology

country: China

institute: The University of Hong Kong

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Porcine Genome Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

organism: Sus scrofa

source_name: coronary arterial endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5-1ug total RNA.

growth_protocol: porcine coronary arterial endothelial cells were brought to primary culture. Cultured endothelial cells for 1 weeks produced cells at passage one (control cells). Serial passaging was performed on a weekly basis until cells at passage four (senescent cells) were reached (test cells). Regenerated endothelial cells (Reg cells) was obtained by regeneration after endothelial denudation in vivo, scraped and cultured without further passage.

extract_protocol: Total RNA was extracted with Rneasy mini kit (Qiagen) performed according to the manufacturer's instructions.

treatment_protocol: Cultured endothelial cells for 1 weeks produced cells at passage one (control cells). Serial passaging was performed on a weekly basis until cells at passage four (senescent cells) were reached (test1 cells). Regenerated endothelial cells (test2 cells) was obtained by regeneration after endothelial denudation in vivo, scraped and cultured without further passage.   Both control and test cells at basal condition were collected for total RNA extraction for microarray analysis.

tag: farm pig/female/3 months


title: MA112: EC-test2-rep 2


title: Sen_virus_vs_mock_12hpi_1

first: Spela

address: Vecna pot 111

description:
Sen_virus_vs_mock_12hpi_1
Biological replicate 1 of 4.

data_processing: The TIFF images were quantified using ArrayPro® Analyzer 4.5 software (Media Cybernetics, USA). Quality control was performed and low quality spots: (i) non-uniform spots (mean (signal) / SD (signal) < 1), (ii) spots with low signal/background ratio (mean (signal) / mean (background) < 1.5) or (iii) spots with low signal to noise ratio (SNR) < 3 were downweighted. Additionally empty or non-validated spots were downweighted (weight flag =0). Data analysis was done in R computing environment (http://www.R-project.org). Background was measured locally. For both channels, signal (trimmed mean of the whole variable spot area) and background (trimmed mean of the spot’s local corners) intensities were calculated. Background was subtracted using the option half. Data was then normalized using loess normalization.

label_protocol: cDNA synthesis and hybridization was carried out using 3DNA Array 900 kit (Genisphere)


title: MA17: EC-test2-rep 1


title: AWBF_BAC_area_T11

description: no additional information

source_name: T11: Lung AWBF - BAC Area

source_name: Male Genomic (reference)


title: PAO1 treated with azithromycin (8 microgram pr. mL) (replicate B)

source_name: PAO1 treated with azithromycin (8 microgram pr. mL) (replicate b)


title: Sen_virus_vs_mock_12hpi_4

description:
Sen_virus_vs_mock_12hpi_4
Biological replicate 4 of 4


title: Sen_virus_vs_mock_12hpi_3

description:
Sen_virus_vs_mock_12hpi_3
Biological replicate 3 of 4


title: mouseTNF_3

description:
8-12-week-old NOD.BDC2.5 transgenic mice were injected i.p. with PBS or 3 ug murine TNFalpha; on alternate days for three weeks. At day 24 of treatment, suspensions of LNs and/or splenocytes were stimulated with the indicated concentration of the mimotope (1047-7 peptide (YVAPVWVRME)) at a density of 7-8 x 106 cells/ml, in a final volume of 1 ml in 24-well plates. After prolonged in vitro culture, cells were harvested 12 hrs post transplantation. CD4+ T cells were purified by labeling of monoclonal Abs of surface markers, Vbeta4-FITC and CD4-PE and enriched by Magnetic beads selection followed by FACS sorting. The purity of CD4+ T cells ranged from 95% to 99% depending on individual CD4 T cells preparation. The data in column represents six independent repeated experiments with half of the slides being reverse replicates. We compared RNA from PBE treated group with TNF treated group without including reference RNA.
Simple annotation: TNF, T-cell
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62092.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2340, 5180; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jason,,Lih Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 14:57:30; Parameter PMT Volts = 550; Parameter Scan Date = 2005-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 36363; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82726]; Parameter Laser Power = 4.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 14:57:30; Parameter PMT Volts = 680; Parameter Scan Date = 2005-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 68586; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82726]; Parameter Laser Power = 3.34; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih


title: Diaphragm 6

status: Public on Jan 24 2008

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Diaphragm 6

hyb_protocol: Standard Affy

scan_protocol: Standard Affy

data_processing: GCOS

source_name: Diaphragm

label_protocol: Standard Affy

extract_protocol: Standard Affy

tag: Young adult SD rat


title: Diaphragm 5

description: Diaphragm 5


title: MMS138TNF3

description:
8-12-week-old NOD.BDC2.5 transgenic mice were injected i.p. with PBS or 3 ug murine TNFalpha; on alternate days for three weeks. At day 24 of treatment, suspensions of LNs and/or splenocytes were stimulated with the indicated concentration of the mimotope (1047-7 peptide (YVAPVWVRME)) at a density of 7-8 x 106 cells/ml, in a final volume of 1 ml in 24-well plates. After prolonged in vitro culture, cells were harvested 12 hrs post transplantation. CD4+ T cells were purified by labeling of monoclonal Abs of surface markers, Vbeta4-FITC and CD4-PE and enriched by Magnetic beads selection followed by FACS sorting. The purity of CD4+ T cells ranged from 95% to 99% depending on individual CD4 T cells preparation. The data in column represents six independent repeated experiments with half of the slides being reverse replicates. We compared RNA from PBE treated group with TNF treated group without including reference RNA.
Simple annotation: TNF, T-cell
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62243.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 8680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jason,,Lih Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.30; Parameter Scan Time = 11:38:10; Parameter PMT Volts = 450; Parameter Scan Date = 2003-04-30; Parameter Pixel Size = 10; Parameter Laser on time = 74151; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.33; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.30; Parameter Scan Time = 11:38:10; Parameter PMT Volts = 520; Parameter Scan Date = 2003-04-30; Parameter Pixel Size = 10; Parameter Laser on time = 74087; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih


title: H3K4me3 ChIP in   E-EML replicate 2 array 1 of 2

status: Public on Apr 29 2008

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: H3K4me3 ChIP in   E-EML replicate 2

hyb_protocol: Agilent hybridization protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B. Images were quantified using Agilent Feature Extraction Software

data_processing: log intensity ratios calculated from of median Cy5/Cy3 signal signal.

source_name: H3K4me3 ChIP in   E-EML replicate 2, labeled with Cyanine-5 (red).

label_protocol: Agilent labeling protocol

growth_protocol: EML cells were plated in 45mls of normal growth medium plus 10U/ml of human erythropoietin (Epo; Ortho) at 75,000 cells/ml in a T75 culture flask and cultured for two days.

extract_protocol:
FACS sorting for ChIP assays: Approximately 3x108 undifferentiated or differentiated EML cells were labeled with either anti-Sca-1-PE (undifferentiated) or anti-c-Kit-FITC (differentiated) for 25 minutes, washed in cold PBS/2% FBS, filtered through 0.30um mesh and FACS sorted. The top 80% of Sca+ undifferentiated cells and the c-Kit- erythroid cells (based on an unstained control) were sorted. The cells maintained at 4C pre-sort and post-sort. Due to the loss of certain histone modifications during the sorting procedure, we placed these cells back in culture in the appropriate growth conditions for 2 hours prior to processing for ChIP assays.
Genomic DNA was extracted following ChIP assays using the SDS/Proteinase K method per the ChIP protocol. During subsequent amplification and labeling steps, DNA was purified using Qiagen MinElute columns.

tag: cells

source_name: H3K4me3 input in   E-EML replicate 2, labeled with Cyanine-3 (green).

extract_protocol: see channel 1


title: MMS033TNF1

description:
8-12-week-old NOD.BDC2.5 transgenic mice were injected i.p. with PBS or 3 ug murine TNFalpha; on alternate days for three weeks. At day 24 of treatment, suspensions of LNs and/or splenocytes were stimulated with the indicated concentration of the mimotope (1047-7 peptide (YVAPVWVRME)) at a density of 7-8 x 106 cells/ml, in a final volume of 1 ml in 24-well plates. After prolonged in vitro culture, cells were harvested 12 hrs post transplantation. CD4+ T cells were purified by labeling of monoclonal Abs of surface markers, Vbeta4-FITC and CD4-PE and enriched by Magnetic beads selection followed by FACS sorting. The purity of CD4+ T cells ranged from 95% to 99% depending on individual CD4 T cells preparation. The data in column represents six independent repeated experiments with half of the slides being reverse replicates. We compared RNA from PBE treated group with TNF treated group without including reference RNA.
Simple annotation: TNF, T-cell
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62242.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 8640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jason,,Lih Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.34; Parameter Scan Time = 11:13:06; Parameter PMT Volts = 460; Parameter Scan Date = 2003-04-30; Parameter Pixel Size = 10; Parameter Laser on time = 74127; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.34; Parameter Scan Time = 11:13:06; Parameter PMT Volts = 550; Parameter Scan Date = 2003-04-30; Parameter Pixel Size = 10; Parameter Laser on time = 74064; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih


title: Diaphragm 4

description: Diaphragm 4


title: H3K4me2 ChIP in   E-EML replicate 2 array 1 of 2

description: H3K4me2 ChIP in   E-EML replicate 2

source_name: H3K4me2 ChIP in   E-EML replicate 2, labeled with Cyanine-5 (red).

source_name: H3K4me2 input in   E-EML replicate 2, labeled with Cyanine-3 (green).


title: MMS035TNF2

description:
8-12-week-old NOD.BDC2.5 transgenic mice were injected i.p. with PBS or 3 ug murine TNFalpha; on alternate days for three weeks. At day 24 of treatment, suspensions of LNs and/or splenocytes were stimulated with the indicated concentration of the mimotope (1047-7 peptide (YVAPVWVRME)) at a density of 7-8 x 106 cells/ml, in a final volume of 1 ml in 24-well plates. After prolonged in vitro culture, cells were harvested 12 hrs post transplantation. CD4+ T cells were purified by labeling of monoclonal Abs of surface markers, Vbeta4-FITC and CD4-PE and enriched by Magnetic beads selection followed by FACS sorting. The purity of CD4+ T cells ranged from 95% to 99% depending on individual CD4 T cells preparation. The data in column represents six independent repeated experiments with half of the slides being reverse replicates. We compared RNA from PBE treated group with TNF treated group without including reference RNA.
Simple annotation: TNF, T-cell
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62241.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 9040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jason,,Lih Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.96; Parameter Scan Time = 12:00:24; Parameter PMT Volts = 600; Parameter Scan Date = 2003-07-30; Parameter Pixel Size = 10; Parameter Laser on time = 81506; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.96; Parameter Scan Time = 12:00:24; Parameter PMT Volts = 610; Parameter Scan Date = 2003-07-30; Parameter Pixel Size = 10; Parameter Laser on time = 81442; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.73; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih

source_name: PBS

source_name: TNF


title: Diaphragm 2

description: Diaphragm 2


title: H3K4me2 ChIP in   E-EML replicate 2 array 2 of 2

description: H3K4me2 ChIP in   E-EML replicate 2


title: Diaphragm 3

description: Diaphragm 3


title: normal human keratinocytes_60hs_2_TNF(rep2)

status: Public on Aug 25 2007

type: other

city: Sao Paulo

first: Lara

last: Termini

state: SP

address: Rua Joao Juliao, 245 - 1th floor

country: Brazil

institute: Ludwig Institute for Cancer Research

description:
normal human keratinocytes_60hs TNF_2
reference: NHFK_3hs in culture_1
amplified RNA

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardt´s ; 10 ug Esperma de salmão,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:5 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:10 min / Washing Number: 2 Washing - Round 3 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:2,5 min / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

molecule: other

tag: normal human keratinocytes

tag: normal human keratinocytes TNF 60hs


title: normal human keratinocytes_60hs_2(rep2)

description:
normal human keratinocytes_60hs in culture_2
reference: NHFK_3hs in culture_1
amplified RNA


title: Diaphragm 1

description: Diaphragm 1


title: normal human keratinocytes_60hs_1(rep1)

description:
normal human keratinocytes_60hs in culture_1
reference: NHFK_3hs in culture_1
amplified RNA


title: normal human keratinocytes_60hs_1_TNF(rep2)

description:
normal human keratinocytes_60hs TNF_1
reference: NHFK_3hs in culture_1
amplified RNA


title: normal human keratinocytes_60hs_1_TNF(rep1)


title: normal human keratinocytes_3hs_1_TNF(rep2)

description:
normal human keratinocytes_3hs TNF_1
reference: NHFK_3hs in culture_1
amplified RNA

tag: normal human keratinocytes TNF 3hs


title: normal human keratinocytes_60hs_1(rep2)


title: normal human keratinocytes_3hs_1_TNF(rep1)


title: normal human keratinocytes_60hs_2_TNF(rep1)


title: normal human keratinocytes_3hs_1(rep2)

description:
normal human keratinocytes_3hs in culture_1
reference: NHFK_3hs in culture_1
amplified RNA


title: normal human keratinocytes_3hs_2(rep2)

description:
normal human keratinocytes_3hs in culture_2
reference: NHFK_3hs in culture_1
amplified RNA


title: HPV16 immortalized keratinocytes_60hs_1_TNF(rep2)

description:
HPV16 immortalizes keratinocytes_60hs TNF_1
reference: NHFK_3hs in culture_1
amplified RNA

tag: HPV16 immortalized keratinocytes TNF 60hs


title: normal human keratinocytes_60hs_2(rep1)


title: normal human keratinocytes_3hs_2(rep1)


title: HPV16 immortalized keratinocytes_3hs_2_TNF(rep1)

description:
HPV16 immortalizes keratinocytes_3hs TNF_2
reference: NHFK_3hs in culture_1
amplified RNA

tag: HPV16 immortalized keratinocytes TNF 3hs


title: mouseTNF_1

description:
8-12-week-old NOD.BDC2.5 transgenic mice were injected i.p. with PBS or 3 ug murine TNFalpha; on alternate days for three weeks. At day 24 of treatment, suspensions of LNs and/or splenocytes were stimulated with the indicated concentration of the mimotope (1047-7 peptide (YVAPVWVRME)) at a density of 7-8 x 106 cells/ml, in a final volume of 1 ml in 24-well plates. After prolonged in vitro culture, cells were harvested 12 hrs post transplantation. CD4+ T cells were purified by labeling of monoclonal Abs of surface markers, Vbeta4-FITC and CD4-PE and enriched by Magnetic beads selection followed by FACS sorting. The purity of CD4+ T cells ranged from 95% to 99% depending on individual CD4 T cells preparation. The data in column represents six independent repeated experiments with half of the slides being reverse replicates. We compared RNA from PBE treated group with TNF treated group without including reference RNA.
Simple annotation: TNF, T-cell
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62090.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jason,,Lih Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.26; Parameter Scan Time = 11:49:02; Parameter PMT Volts = 560; Parameter Scan Date = 2005-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 36369; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.26; Parameter Scan Time = 11:49:02; Parameter PMT Volts = 590; Parameter Scan Date = 2005-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 109504; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.69; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jason,,Lih


title: HPV16 immortalized keratinocytes_3hs_2_TNF(rep2)


title: normal human keratinocytes_3hs_2_TNF(rep1)

description:
normal human keratinocytes_3hs TNF_2
reference: NHFK_3hs in culture_1
amplified RNA


title: HPV16 immortalized keratinocytes_60hs_2_TNF(rep2)

description:
HPV16 immortalizes keratinocytes_60hs TNF_2
reference: NHFK_3hs in culture_1
amplified RNA


title: HPV16 immortalized keratinocytes_3hs_1_TNF(rep2)

description:
HPV16 immortalizes keratinocytes_3hs TNF_1
reference: NHFK_3hs in culture_1
amplified RNA


title: HPV16 immortalized keratinocytes_60hs_2_TNF(rep1)


title: normal human keratinocytes_3hs_1(rep1)


title: H3K4me3 ChIP in   E-EML replicate 2 array 2 of 2

description: H3K4me3 ChIP in   E-EML replicate 2


title: HPV16 immortalized keratinocytes_60hs_1_TNF(rep1)


title: HPV16 immortalized keratinocytes_60hs_1(rep1)

description:
HPV16 immortalizes keratinocytes_60hs in culture_1
reference: NHFK_3hs in culture_1
amplified RNA

tag: HPV16 immortalized keratinocytes