title: F7


title: slide18b-2848-2916-wtmallarddec03

status: Public on Dec 06 2006

type: RNA

city: Guelph

first: Wenjing

last: Tao

state: ON

address: Gordon street

department: Department of Pathobiology

country: Canada

institute: University of Guelph

description: Feature symbols and assigned values: Bad spot -100 X Absent -75 (absent spots are assigned based on gene list) Not found -50 | Not flagged 0 Good spot 100

hyb_protocol: (5) Prehybridization: Combine 80 μl DIG Easy Hyb, 4 μl of blocking RNA/DNA, 65ºC for 2 min. Let the solution cool for 2 min at room temperature. Pipette 30-50μl prehyb buffer onto the chip, place the array chip into a slide box containing a small amount of DIG Easy Hyb, wrap the slide box with plastic wrap and place into a incubator, incubate at 42ºC for 45 min 2. Wash slides in room temperature DEPC-H2O, shaker for 10 min 3. Dip slides in room temperature isopropanol and spin dry in centrifuge for 5 min slides should be used immediately and should not dry for more than 1 hr (6) Hybridization: 1. Reused each labeled probe in 5μl of 2xHybridization buffer (make fresh) 2. Combine 5μl of each of purified Cy3- and Cy5-labeled probes, mix well 3. Add 4μl COT1-DNA (1μg/μl) 4. Add 5μl Poly(A)-DNA (5μg/μl) 5. Add 1μl tRNA (10μg/μl) 6. Heat probe mixture at 95ºC for 3 min to denature 7. Centrifuge probe for 1 min at maximum speed 8. Apply labeled probes to prehybridized microarray slide and coverslip (22 X 22 mm) 9. Place sealed slide box in a 42ºC incubator, and incubate for 16-20 hr (7) Washing: Prepare some pre-warmed (50ºC) 1X SSC + 0.1% SDS, also prepare some room temperature 1X SSC 1. Remove array from box and dip it a few times into 1X SSC. Once the cover slip has been removed, place the chip in the side holder and put the holder into the dish with 1X SSC + 0.1% SDS, leave the chip in 1X SSC + 0.1% SDS for 15 minutes, with a quick shake at 7.5 minutes. When 15 minutes is up, move the chip to a new dish of 1X SSC + 0.1% SDS, leave 15 minutes, with quick shake at 7.5 minutes. Repeat same wash in another new dish. 2. Wash slide in 1X SSC at room temperature to remove traces of SDS. 3. If necessary, do an additional wash in room temperature 0.1XSSC if you find that salt is precipitating on the chip. 4. Place slide into a clean slide box that has filter paper lining the bottom. Spin the slide box at 500 rpm for 5 min. 5. Scan slide if possible the same day

scan_protocol: Turn on the scanner and open the GenePix Pro software. Warm up the scanner for 15 min before image acquisition. Slide the scanner door open. Gently lift the tab on the front of slide holder to open the lid. Pull open the adjustment arm (lever) on the left of the slide holder with one finger, and insert the slide array side down (label out, face down) into the slide holder. Flick the lever slightly to ensure proper positioning of the slide. Gently close the slide holder lid until it snaps shut, and close the door. Click on the hardware button on the lower right, set the PMT ro 600V (default) for both channels (635 for Cy5 and Alexa 647, and 532 for Cy3 and Alexa 546). Perform a low resolution scan of the slide using the Preview Scan button (fast forward). Use the Histogram tab on the top to adjust the minimum intensity to 1000 and the maximum intensity to 65000. This is to eliminate background as most background is at an intensity of around 300-500. Observe the relative intensities of both channels (this is the ratio of the dyes, and making sure that the Log Axis box is checked). If necessary, adjust the PMT settings on the fly to achieve a color balance (ratio ~1.0). We routinely use a higher PMT setting for Cy5 (e.g., 670) than Cy3 (e.g., 600). Define the array location for high resolution scan using the View Scan Area button on the left. The box can be re-positioned and re-sized by clicking-and-dragging with the mouse. Click the Data Scan button to execute a high resolution scan of the specific area. Use the Histogram tab to monitor the intensities of both channels. If they do not overlap, click the Stop button and readjust the PMT settings. To save the image, click the File button and select Save Images. Save images as Multi-image TIFF Files and name your file. GenePix automatically adds the wavelength of the image as a suffix to the file name. Click the histogram tab, check the ratio. We want it to be around 1.0. Once the ratio of image is near 1.0, then select the elect button. After the scanner has stopped making noise, open the scanner and remove the array slide. Image Analysis After finish all scans, turn off the scanner and power supply. Close the current program. Click on the GenePix pro demo icon. Click the File… button and select Open Images to open previously saved images. Navigate to the directory that contains the previously saved TIFF images. Hold down the <Ctrl> key to select a pair of images from the wavelengths 635 and 532. Image display: Brightness/Contrast; Zoom Mode; Undo Zoom; Full Scale, etc Load the GAL (GenePix Array List) file containing gene list information by clicking the File button, and select the Load Array List command. Select the gal file and click open. This procedure automatically constructs blocks that match the number, size and positioning of printed features and assigns identifiers to each spot. Use the arrow keys to move the array grids to align with the spots as well as possible (no need to be perfect). Press F5 key to Find Features automatically. Right click to change between Block mode or Feature mode to fine-tune the alignment using the arrow keys (block-by-block). Press F5 to re-match the features. After the alignment is done, examine each grid. Using the Feature mode, flag spots that are bad (e.g., contaminated) or not found (e.g., weak) and make necessary adjustments. Select the spot and right click to apply the desired function (Good, Bad or Not found). To re-set feature positions, right click and select Clear Nudges. Flags can be re-set thesame way. Similar spots can be handled simultaneously by dragging a region around them. Select the “analyze” button, the columns of data should appear. Select the save as button and save the file. This will generate a gpr file (one per image) that can be used in the future (e.g., no need to redo the alignment), and 3 jpg (653, 532 and ratio) files.

data_processing: Genepix

molecule: total RNA

organism: Bos taurus

source_name: healthy

label_protocol: Indirect-labelling with cy3: (1) RT Reaction: After Trizol extraction and RNeasy purification, RNA is resuspended in H2O. After taking samples out from –80°C freezer, heat RNA samples to 50-65ºC (water bath) for 10 min and cool to RT for 10 min before starting. Bring water bath down to 42°C. Take 10μg total RNA and add DEPC H2O to get final amount of 14μl Add AncT primer (3μg/μl) 2μl Total volume 16μl Incubate at 70°C (heat block) for 10 min and chill on ice for 5 min Add: 5X First Strand Buffer 6μl 0.1M DTT 3μl 5X aa-dNTP mix 2.0μl SSII Reverse Transcriptase 1.5μl Rnase OUT 1.5μl Total volume 30μl Incubate at 42°C (water bath) for 3 hr. (Can be longer, e.g. over night) (2) Labeling Reaction: 1. to each labeling reaction add of 500mM EDTA (pH8.0) 10μl 2. vortex 3. add of 1M NaOH 10μl 4. vortex and spin briefly 5. incubate at 65°C (heat block) for 20 min to hydrolyze RNA, then cool to R/T 6. spin briefly 7. to neutralize, add 1M HCL 10μl vortex and spin briefly 8. perform probe purification with Qiagen PCR spin columns: a. add 300μl PB buffer to reaction, mix with pipette, and transfer to QIAquick column b. spin at maximum speed for 1 min, discard flow through c. wash with 740μl phosphate wash buffer (home-made buffer, NOT from kit) d. spin at maximum speed for 1 min e. empty collection tube and repeat wash steps c and d f. empty collection tube and spin at maximum speed for 1 min g. transfer column to a fresh tube (cut off caps), elute with 30μl elution buffer (home-made KPO4, NOT from kit) with 1 min incubation followed by spin at maximum speed for 1 min h. repeat elution step g, transfer to new tube i. speedvac dry (~ 40 minutes) (heater on middle) 9. Cy dye coupling a. resuspend the cDNA in 4.5μl 0.1M carbonate buffer, pH9.0 (< 1 month old) b. add 4.5μl NHS-Cy dyes c. incubate the reactions in dark for 2 hours at room temperature make prehyb. buffer and warm to 42°C Set heat block to 95°C (Alexa dye labeling: dissolve an aliquot Alexa 546 or 647 in 9 ul DMSO, pipette 5 ul Alexa dye to each cDNA in 4.5 ul of 0.1M carbonate buffer, pH9.0. Incubate both samples for 1-2 hours at room temperature in dark) (3) Purification: 1. Add 35μl 100mM NaOAc pH 5.2 to the reaction 2. Add 250μl PB buffer to reaction and follow QIAquick PCR purification protocol: a. Apply reaction volume to QIAquick spin column and centrifuge for 1 minute b. Discard flow-through, should be colored c. Add 0.74ml buffer PE (as provided with kit) to column and centrifuge for 1 minute d. Discard flow-through and centrifuge for an additional 1-minute at maximum speed e. Place QIAquick column in a clean 1.5ml microcentrifuge tube f. Elute twice with 30μl EB using 1-minute incubation time before centrifugation (eluted sample should look colored and filter should be white) g. Take 1μl of sample for dye incorporation analysis h. Speedvac dry sample (~ 40 minutes) (heat setting to middle) Alternative: precipitate DNA with 1/10 volume 3M sodium acetate, 1/100 volume glycogen, final conc. of 65% ethanol. (4) Dye Incorporation Analysis: 1. Take 1μl of sample for dye incorporation analysis 2. Measure absorbance at 260nm, 550nm (Cy3), for Cy3 incorporation: nucleotide/dye = 17.1*OD260/OD550 150pmole/slide is optimal for hybridization; nucleotide/dye should be < 50

extract_protocol: TRIzol reagent

tag: no evidence of S. aureus mastitis

source_name: mastitis

label_protocol: indirect-labelled with cy5: (1) RT Reaction: After Trizol extraction and RNeasy purification, RNA is resuspended in H2O. After taking samples out from –80°C freezer, heat RNA samples to 50-65ºC (water bath) for 10 min and cool to RT for 10 min before starting. Bring water bath down to 42°C. Take 10μg total RNA and add DEPC H2O to get final amount of 14μl Add AncT primer (3μg/μl) 2μl Total volume 16μl Incubate at 70°C (heat block) for 10 min and chill on ice for 5 min Add: 5X First Strand Buffer 6μl 0.1M DTT 3μl 5X aa-dNTP mix 2.0μl SSII Reverse Transcriptase 1.5μl Rnase OUT 1.5μl Total volume 30μl Incubate at 42°C (water bath) for 3 hr. (Can be longer, e.g. over night) (2) Labeling Reaction: 1. to each labeling reaction add of 500mM EDTA (pH8.0) 10μl 2. vortex 3. add of 1M NaOH 10μl 4. vortex and spin briefly 5. incubate at 65°C (heat block) for 20 min to hydrolyze RNA, then cool to R/T 6. spin briefly 7. to neutralize, add 1M HCL 10μl vortex and spin briefly 8. perform probe purification with Qiagen PCR spin columns: a. add 300μl PB buffer to reaction, mix with pipette, and transfer to QIAquick column b. spin at maximum speed for 1 min, discard flow through c. wash with 740μl phosphate wash buffer (home-made buffer, NOT from kit) d. spin at maximum speed for 1 min e. empty collection tube and repeat wash steps c and d f. empty collection tube and spin at maximum speed for 1 min g. transfer column to a fresh tube (cut off caps), elute with 30μl elution buffer (home-made KPO4, NOT from kit) with 1 min incubation followed by spin at maximum speed for 1 min h. repeat elution step g, transfer to new tube i. speedvac dry (~ 40 minutes) (heater on middle) 9. Cy dye coupling a. resuspend the cDNA in 4.5μl 0.1M carbonate buffer, pH9.0 (< 1 month old) b. add 4.5μl NHS-Cy dyes c. incubate the reactions in dark for 2 hours at room temperature make prehyb. buffer and warm to 42°C Set heat block to 95°C (Alexa dye labeling: dissolve an aliquot Alexa 546 or 647 in 9 ul DMSO, pipette 5 ul Alexa dye to each cDNA in 4.5 ul of 0.1M carbonate buffer, pH9.0. Incubate both samples for 1-2 hours at room temperature in dark) (3) Purification: 1. Add 35μl 100mM NaOAc pH 5.2 to the reaction 2. Add 250μl PB buffer to reaction and follow QIAquick PCR purification protocol: a. Apply reaction volume to QIAquick spin column and centrifuge for 1 minute b. Discard flow-through, should be colored c. Add 0.74ml buffer PE (as provided with kit) to column and centrifuge for 1 minute d. Discard flow-through and centrifuge for an additional 1-minute at maximum speed e. Place QIAquick column in a clean 1.5ml microcentrifuge tube f. Elute twice with 30μl EB using 1-minute incubation time before centrifugation (eluted sample should look colored and filter should be white) g. Take 1μl of sample for dye incorporation analysis h. Speedvac dry sample (~ 40 minutes) (heat setting to middle) Alternative: precipitate DNA with 1/10 volume 3M sodium acetate, 1/100 volume glycogen, final conc. of 65% ethanol. (4) Dye Incorporation Analysis: 1. Take 1μl of sample for dye incorporation analysis 2. Measure absorbance at 260nm, 650nm (Cy5) for Cy5 incorporation: nucleotide/dye = 28.5*OD260/OD650 150pmole/slide is optimal for hybridization; nucleotide/dye should be < 50

tag: Staph aureus mastitis


title: Canary 1a; green: whole brain, red: HVC

city: New York

first: XiaoChing

last: Li

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

hyb_protocol: 42 degrees overnight, Corning hybridization buffer

scan_protocol: 647 nm and 555 nm

data_processing: log2 of fold change (comparison of background-subtracted experimental intensity and LOWESS-normalized reference intensity)

organism: Serinus canaria

source_name: Green: whole brain

label_protocol: cDNA probe by reverse transcription

extract_protocol: Qiagen RNeasy Micro Kit (Cat. No. 74004)

tag: adult male canary

source_name: Red: HVC


title: slide43c-2834-2883-wtmallard

source_name: healthy control

source_name: Mastitis


title: slide21b-2924-2947-wtmallarddec03

source_name: healthy contro.l


title: Canary 1b; green: whole brain, red: HVC


title: F8

type: genomic

city: Vancouver

first: Kendy

last: Wong

state: British Columbia

address: 675 West 10th Avenue

department: Cancer Genetics

institute: BC Cancer Research Center

description:
cyanine 3 = sample
cyanine 5 = reference

data_processing: three-step normalization procedure; (Khojasteh et al BMC Bioinformatics 2005;6:274)

label: Cyanine 3

molecule: genomic DNA

organism: Homo sapiens

tag: B-lymphocyte cell line DNA, a daughter of pedigree XC01423

label: Cyanine 5

source_name: Mref

extract_protocol: QIAamp DNA Blood Maxi Kit (QIAGEN Inc.)

tag: single male reference genomic DNA


title: velvetleaf/corn competition W4RC4B

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

hyb_protocol: Probe was resuspended in 24.6 ul water, 7.2 ul of 2%SDS, 7.65 ul 20XSSC, and 3.75 ul of yeast tRNA (2ug/ul). Probe was denatured at 95 C for 5 minutes and placed on array. Array was hybridized overnight at 60 C. Array was washed 2X in 0.1XSSC, 0.1% SDS at room temp for 5 min. and 2X in 0.1XSSC for 5 min at room temp.  The array was spun dry.

scan_protocol: Array was scanned in an Affy 428 scanner using Jaguar software.

data_processing: Raw data was loess normalized using the GeneMaths XT software program and the log2 of the normalized ratio was generated.

organism: Abutilon theophrasti

source_name: Velvetleaf in monoculture

label_protocol: Two step labeling of 30 ug total RNA using invitrogen ARES alexa Fluor labeling kit according to manufacturers protocol.

extract_protocol: Chang, S., J. Puryear, and J. Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.

treatment_protocol: Velvetleaf was sown on May 8, 2006 alone or with corn (DKC46-22) at Aurora, SD on a Brandt silty clay loam soil (fine-silty, mixed superactive, frigid Calcic Hapludoll).  The sand, silt, and clay contents were 390, 383, and 226 g kg-1, respectively, with a pH of 6.0 and organic matter content of 35 g kg-1. Velvetleaf seed was  planted about 1.5 cm deep using a seed drill either alone or in the interrow area of corn  about 20 cm from the crop row. Granular urea was broadcast at 224 kg N ha-1 after planting. Weed management for species other than velvetleaf consisted of a glyphosate application as a burn-down treatment prior to plant emergence and hand removal for the rest of the season. There was some variability in the density of velvetleaf between plots due to uneven germination, however, in general, velvetleaf density was  about 6 plants m-2 (ranging from 4 to 8 plants m-2) after germination. Treatments were placed in  randomized complete block design with four replicates. Plots were six m long by four rows wide with a row spacing of 76 cm with four replications per treatment.  On June 22nd between 1:00 and 2:00 PM, the apical meristem and all of the young leaves (up to 6 cm in diameter) were collected from 4 individual velvetleaf plants within each treatment plot. The samples from within each plot were pooled and immediately frozen in liquid N¬2.

tag: wild seed stock

source_name: Weed with corn

treatment_protocol: Velvetleaf was sown on May 8, 2006 alone or with corn (DKC46-22) at Aurora, SD on a Brandt silty clay loam soil (fine-silty, mixed superactive, frigid Calcic Hapludoll).  The sand, silt, and clay contents were 390, 383, and 226 g kg-1, respectively, with a pH of 6.0 and organic matter content of 35 g kg-1. Corn was planted at a population of about 24,000 plants ha-1.  Velvetleaf seed was  planted about 1.5 cm deep using a seed drill either alone or in the interrow area of corn  about 20 cm from the crop row. Granular urea was broadcast at 224 kg N ha-1 after planting. Weed management for species other than velvetleaf consisted of a glyphosate application as a burn-down treatment prior to plant emergence and hand removal for the rest of the season. There was some variability in the density of velvetleaf between plots due to uneven germination, however, in general, velvetleaf density was  about 6 plants m-2 (ranging from 4 to 8 plants m-2) after germination. Treatments were placed in  randomized complete block design with four replicates. Plots were six m long by four rows wide with a row spacing of 76 cm with four replications per treatment.  On June 22nd between 1:00 and 2:00 PM, the apical meristem and all of the young leaves (up to 6 cm in diameter) were collected from 4 individual velvetleaf plants within each treatment plot. The samples from within each plot were pooled and immediately frozen in liquid N¬2.


title: slide47-2970-3028-wtmallard


title: Brain_totalRNA_no_immunoprecipitation_Biorep2

city: Boston

first: Yanmei

last: Huang

state: MA

address: 136 Harrison Ave, A305B

department: Neuroscience

institute: Tufts University School of Medicine

description: The amount of RNAs captured by the immunoprecipitation was very small. In order to match with the immunoprecipitated sample, similar amount of RNA from this total RNA control sample were labeled and hybridized to the array. Thus the average intensity on the array is relatively low.

hyb_protocol: Around 3.33 ug of labeled RNAs were hybridized to the Drosophila genome array following standard protocol provided by Affymetrix. The array was washed and stained on a Affymetrix Fluidics Station 400 using standard protocols.

scan_protocol: An Agilent GeneArray Scanner was used to scan the array. Pixel size: 3 um, filter: 570nm, number of scan: 2

data_processing: Data generated by MAS5.0 and scaled to a target intensity of 5

label: Biotin

molecule: other

organism: Drosophila melanogaster

source_name: Drosophila pharate adult brain, total RNA

label_protocol: Affymetrix one cycle cDNA synthesis kit and and IVT labeling kit were used to label the RNAs following the standard protocols provided by Affymetrix.

growth_protocol: Fly cultures were grown in 25oC on standard media made from receipt provided by the Bloomington stock center.

extract_protocol: Acidic phenol:chlorophorm (Ambion) were used to extract RNA from the treated sample. Extracted RNAs were precipitated with isopropyl-alcohol and glycogen and dissolved in RNase-free water.

treatment_protocol: Tissue lysate was obtained by homogenization and mild sonication.

tag: Hand-dissected brain tissue from pharate adult of the Canton-S strain of D. melanogaster.


title: slide45c-2929-2914-wtmallard


title: slide20b-2916-2848-wtmallarddec03

source_name: Healthy control


title: F5

tag: B-lymphocyte cell line DNA, father of pedigree XC01423


title: Brain_immunoprecipitated_with_anti-LARK_Biorep2

description: The amount of RNAs captured by the immunoprecipitation was very small, thus the average intensity on the array is relatively low.

hyb_protocol: Around 3.31 ug of labeled RNAs were hybridized to the Drosophila genome array following standard protocol provided by Affymetrix. The array was washed and stained on a Affymetrix Fluidics Station 400 using standard protocols.

source_name: Drosophila pharate adult brain, immunoprecipitated with anti-LARK

extract_protocol: After immunoprecipitation, the beads, together with the coated LARK antibody and the immunoprecipitated LARK-RNP, were treated with proteinase K at 37oC for 30min. Acidic phenol:chlorophorm (Ambion) were used to extract RNA from the treated sample. Extracted RNAs were precipitated with isopropyl-alcohol and glycogen and dissolved in RNase-free water.

treatment_protocol: Tissue lysate was obtained by homogenization and mild sonication. Anti-LARK antibody was used to immunoprecipitate LARK-RNP and RNAs were extracted from the LARK-RNP sample.


title: velvetleaf/corn competition W1RC2B


title: F4

tag: B-lymphocyte cell line DNA, maternal grandmother of pedigree XC01423


title: slide16-2947-2924-wtmallarddec03


title: F2

tag: B-lymphocyte cell line DNA, paternal grandmother of pedigree XC01423


title: Brain_totalRNA_no_immunoprecipitation_Biorep1

hyb_protocol: Around 2.35 ug of labeled RNAs were hybridized to the Drosophila genome array following standard protocol provided by Affymetrix. The array was washed and stained on a Affymetrix Fluidics Station 400 using standard protocols.


title: F1

tag: B-lymphocyte cell line DNA, paternal grandfather of pedigree XC01423


title: velvetleaf/corn competition W2RC2B


title: slide41d-2970-3028-wtmallard


title: slide44-2834-2883-wtmallard

source_name: Healty control


title: slide15b-3011-3072-wtmallarddec03

description:
Feature symbols and assigned values:
Bad spot -100 X
Absent -75 (absent spots are assigned based on gene list)
Not found -50 |
Not flagged 0
Good spot 100

hyb_protocol: (5) Prehybridization: Combine 80 μl DIG Easy Hyb, 4 μl of blocking RNA/DNA, 65ºC for 2 min.  Let the solution cool for 2 min at room temperature.  Pipette 30-50μl prehyb buffer onto the chip, place the array chip into a slide box containing a small amount of DIG Easy Hyb, wrap the slide box with plastic wrap and place into a incubator, incubate at 42ºC for 45 min 2. Wash slides in room temperature DEPC-H2O, shaker for 10 min 3. Dip slides in room temperature isopropanol and spin dry in centrifuge for 5 min slides should be used immediately and should not dry for more than 1 hr (6) Hybridization: 1. Reused each labeled probe in 5μl of 2xHybridization buffer (make fresh) 2. Combine 5μl of each of purified Cy3- and Cy5-labeled probes, mix well 3. Add 4μl COT1-DNA (1μg/μl) 4. Add 5μl Poly(A)-DNA (5μg/μl) 5. Add 1μl tRNA (10μg/μl) 6. Heat probe mixture at 95ºC for 3 min to denature 7. Centrifuge probe for 1 min at maximum speed 8. Apply labeled probes to prehybridized microarray slide and coverslip (22 X 22 mm) 9. Place sealed slide box in a 42ºC incubator, and incubate for 16-20 hr (7) Washing: Prepare some pre-warmed (50ºC) 1X SSC + 0.1% SDS, also prepare some room temperature 1X SSC 1. Remove array from box and dip it a few times into 1X SSC.  Once the cover slip has been removed, place the chip in the side holder and put the holder into the dish with 1X SSC + 0.1% SDS, leave the chip in 1X SSC + 0.1% SDS for 15 minutes, with a quick shake at 7.5 minutes.  When 15 minutes is up, move the chip to a new dish of 1X SSC + 0.1% SDS, leave 15 minutes, with quick shake at 7.5 minutes.  Repeat same wash in another new dish. 2. Wash slide in 1X SSC at room temperature to remove traces of SDS. 3. If necessary, do an additional wash in room temperature 0.1XSSC if you find that salt is precipitating on the chip. 4. Place slide into a clean slide box that has filter paper lining the bottom. Spin the slide box at 500 rpm for 5 min. 5. Scan slide if possible the same day

scan_protocol: Turn on the scanner and open the GenePix Pro software. Warm up the scanner for 15 min before image acquisition. Slide the scanner door open. Gently lift the tab on the front of slide holder to open the lid.  Pull open the adjustment arm (lever) on the left of the slide holder with one finger, and insert the slide array side down (label out, face down) into the slide holder. Flick the lever slightly to ensure proper positioning of the slide. Gently close the slide holder lid until it snaps shut, and close the door. Click on the hardware button on the lower right, set the PMT ro 600V (default) for both channels (635 for Cy5 and Alexa 647,  and 532 for Cy3 and Alexa 546). Perform a low resolution scan of the slide using the Preview Scan button (fast forward). Use the Histogram tab on the top to adjust the minimum intensity to 1000 and the maximum intensity to 65000.  This is to eliminate background as most background is at an intensity of around 300-500.  Observe the relative intensities of both channels (this is the ratio of the dyes, and making sure that the Log Axis box is checked). If necessary, adjust the PMT settings on the fly to achieve a color balance (ratio ~1.0). We routinely use a higher PMT setting for Cy5 (e.g., 670) than Cy3 (e.g., 600). Define the array location for high resolution scan using the View Scan Area button on the left. The box can be re-positioned and re-sized by clicking-and-dragging with the mouse. Click the Data Scan button to execute a high resolution scan of the specific area. Use the Histogram tab to monitor the intensities of both channels. If they do not overlap, click the Stop button and readjust the PMT settings. To save the image, click the File button and select Save Images. Save images as Multi-image TIFF Files and name your file.  GenePix automatically adds the wavelength of the image as a suffix to the file name. Click the histogram tab, check the ratio.  We want it to be around 1.0.  Once the ratio of image is near 1.0, then select the elect button.  After the scanner has stopped making noise, open the scanner and remove the array slide. Image Analysis After finish all scans, turn off the scanner and power supply.  Close the current program.  Click on the GenePix pro demo icon.  Click the File… button and select Open Images to open previously saved images. Navigate to the directory that contains the previously saved TIFF images. Hold down the <Ctrl> key to select a pair of images from the wavelengths 635 and 532. Image display: Brightness/Contrast; Zoom Mode; Undo Zoom; Full Scale, etc Load the GAL (GenePix Array List) file containing gene list information by clicking the File button, and select the Load Array List command. Select the gal file and click open. This procedure automatically constructs blocks that match the number, size and positioning of printed features and assigns identifiers to each spot. Use the arrow keys to move the array grids to align with the spots as well as possible (no need to be perfect). Press F5 key to Find Features automatically. Right click to change between Block mode or Feature mode to fine-tune the alignment using the arrow keys (block-by-block). Press F5 to re-match the features. After the alignment is done, examine each grid. Using the Feature mode, flag spots that are bad (e.g., contaminated) or not found (e.g., weak) and make necessary adjustments. Select the spot and right click to apply the desired function (Good, Bad or Not found). To re-set feature positions, right click and select Clear Nudges. Flags can be re-set thesame way. Similar spots can be handled simultaneously by dragging a region around them. Select the “analyze” button, the columns of data should appear.  Select the save as button and save the file. This will generate a gpr file (one per image) that can be used in the future (e.g., no need to redo the alignment), and 3 jpg (653, 532 and ratio) files.

label_protocol:
Indirect-labelling with cy3:
(1) RT Reaction:
After Trizol extraction and RNeasy purification, RNA is resuspended in H2O. After taking samples out from –80°C freezer, heat RNA samples to 50-65ºC (water bath) for 10 min and cool to RT for 10 min before starting. Bring water bath down to 42°C.  Take 10μg total RNA and add DEPC H2O to get final amount of 14μl
Add AncT primer (3μg/μl) 2μl
Total volume 16μl
Incubate at 70°C (heat block) for 10 min and chill on ice for 5 min
Add:
5X First Strand Buffer 6μl
0.1M DTT 3μl
5X aa-dNTP mix 2.0μl
SSII Reverse Transcriptase 1.5μl
Rnase OUT 1.5μl
Total volume 30μl
Incubate at 42°C (water bath) for 3 hr. (Can be longer, e.g. over night)
(2) Labeling Reaction:
1. to each labeling reaction add of 500mM EDTA (pH8.0) 10μl
2. vortex
3. add of 1M NaOH 10μl
4. vortex and spin briefly
5. incubate at 65°C (heat block) for 20 min to hydrolyze RNA, then cool to R/T
6. spin briefly
7. to neutralize, add 1M HCL 10μl
vortex and spin briefly
8. perform probe purification with Qiagen PCR spin columns:
a. add 300μl PB buffer to reaction, mix with pipette, and transfer to QIAquick column
b. spin at maximum speed for 1 min, discard flow through
c. wash with 740μl phosphate wash buffer (home-made buffer, NOT from kit)
d. spin at maximum speed for 1 min
e. empty collection tube and repeat wash steps c and d
f. empty collection tube and spin at maximum speed for 1 min
g. transfer column to a fresh tube (cut off caps), elute with 30μl elution buffer
(home-made KPO4, NOT from kit) with 1 min incubation followed by spin at
maximum speed for 1 min
h. repeat elution step g, transfer to new tube
i. speedvac dry (~ 40 minutes) (heater on middle)
9. Cy dye coupling
a. resuspend the cDNA in 4.5μl 0.1M carbonate buffer, pH9.0 (< 1 month old)
b. add 4.5μl NHS-Cy dyes
c. incubate the reactions in dark for 2 hours at room temperature
make prehyb. buffer and warm to 42°C
Set heat block to 95°C
(Alexa dye labeling:  dissolve an aliquot Alexa 546 or 647 in 9 ul DMSO, pipette 5 ul Alexa dye to each cDNA in 4.5 ul of 0.1M carbonate buffer, pH9.0.  Incubate both samples for 1-2 hours at room temperature in dark)
(3) Purification:
1. Add 35μl 100mM NaOAc pH 5.2 to the reaction
2. Add 250μl PB buffer to reaction and follow QIAquick PCR purification protocol:
a. Apply reaction volume to QIAquick spin column and centrifuge for 1 minute
b. Discard flow-through, should be colored
c. Add 0.74ml buffer PE (as provided with kit) to column and centrifuge for 1 minute
d. Discard flow-through and centrifuge for an additional 1-minute at maximum speed
e. Place QIAquick column in a clean 1.5ml microcentrifuge tube
f. Elute twice with 30μl EB using 1-minute incubation time before centrifugation
(eluted sample should look colored and filter should be white)
g. Take 1μl of sample for dye incorporation analysis
h. Speedvac dry sample (~ 40 minutes) (heat setting to middle)
Alternative: precipitate DNA with 1/10 volume 3M sodium acetate, 1/100 volume glycogen, final conc. of 65% ethanol.
(4) Dye Incorporation Analysis:
1. Take 1μl of sample for dye incorporation analysis
2. Measure absorbance at 260nm, 550nm (Cy3),
for Cy3 incorporation: nucleotide/dye = 17.1*OD260/OD550
150pmole/slide is optimal for hybridization; nucleotide/dye should be < 50

label_protocol:
indirect-labelled with cy5:
(1) RT Reaction:
After Trizol extraction and RNeasy purification, RNA is resuspended in H2O. After taking samples out from –80°C freezer, heat RNA samples to 50-65ºC (water bath) for 10 min and cool to RT for 10 min before starting. Bring water bath down to 42°C.  Take 10μg total RNA and add DEPC H2O to get final amount of 14μl
Add AncT primer (3μg/μl) 2μl
Total volume 16μl
Incubate at 70°C (heat block) for 10 min and chill on ice for 5 min
Add:
5X First Strand Buffer 6μl
0.1M DTT 3μl
5X aa-dNTP mix 2.0μl
SSII Reverse Transcriptase 1.5μl
Rnase OUT 1.5μl
Total volume 30μl
Incubate at 42°C (water bath) for 3 hr. (Can be longer, e.g. over night)
(2) Labeling Reaction:
1. to each labeling reaction add of 500mM EDTA (pH8.0) 10μl
2. vortex
3. add of 1M NaOH 10μl
4. vortex and spin briefly
5. incubate at 65°C (heat block) for 20 min to hydrolyze RNA, then cool to R/T
6. spin briefly
7. to neutralize, add 1M HCL 10μl
vortex and spin briefly
8. perform probe purification with Qiagen PCR spin columns:
a. add 300μl PB buffer to reaction, mix with pipette, and transfer to QIAquick column
b. spin at maximum speed for 1 min, discard flow through
c. wash with 740μl phosphate wash buffer (home-made buffer, NOT from kit)
d. spin at maximum speed for 1 min
e. empty collection tube and repeat wash steps c and d
f. empty collection tube and spin at maximum speed for 1 min
g. transfer column to a fresh tube (cut off caps), elute with 30μl elution buffer
(home-made KPO4, NOT from kit) with 1 min incubation followed by spin at
maximum speed for 1 min
h. repeat elution step g, transfer to new tube
i. speedvac dry (~ 40 minutes) (heater on middle)
9. Cy dye coupling
a. resuspend the cDNA in 4.5μl 0.1M carbonate buffer, pH9.0 (< 1 month old)
b. add 4.5μl NHS-Cy dyes
c. incubate the reactions in dark for 2 hours at room temperature
make prehyb. buffer and warm to 42°C
Set heat block to 95°C
(Alexa dye labeling:  dissolve an aliquot Alexa 546 or 647 in 9 ul DMSO, pipette 5 ul Alexa dye to each cDNA in 4.5 ul of 0.1M carbonate buffer, pH9.0.  Incubate both samples for 1-2 hours at room temperature in dark)
(3) Purification:
1. Add 35μl 100mM NaOAc pH 5.2 to the reaction
2. Add 250μl PB buffer to reaction and follow QIAquick PCR purification protocol:
a. Apply reaction volume to QIAquick spin column and centrifuge for 1 minute
b. Discard flow-through, should be colored
c. Add 0.74ml buffer PE (as provided with kit) to column and centrifuge for 1 minute
d. Discard flow-through and centrifuge for an additional 1-minute at maximum speed
e. Place QIAquick column in a clean 1.5ml microcentrifuge tube
f. Elute twice with 30μl EB using 1-minute incubation time before centrifugation
(eluted sample should look colored and filter should be white)
g. Take 1μl of sample for dye incorporation analysis
h. Speedvac dry sample (~ 40 minutes) (heat setting to middle)
Alternative: precipitate DNA with 1/10 volume 3M sodium acetate, 1/100 volume glycogen, final conc. of 65% ethanol.
(4) Dye Incorporation Analysis:
1. Take 1μl of sample for dye incorporation analysis
2. Measure absorbance at 260nm, 650nm (Cy5)
for Cy5 incorporation: nucleotide/dye = 28.5*OD260/OD650
150pmole/slide is optimal for hybridization; nucleotide/dye should be < 50


title: slide46c-3011-3072-wtmallard


title: velvetleaf/corn competition C4RW1B

treatment_protocol: Velvetleaf was sown on May 8, 2006 alone or with corn (DKC46-22) at Aurora, SD on a Brandt silty clay loam soil (fine-silty, mixed superactive, frigid Calcic Hapludoll).  The sand, silt, and clay contents were 390, 383, and 226 g kg-1, respectively, with a pH of 6.0 and organic matter content of 35 g kg-1. Corn was planted at a population of about 24,000 plants ha-1.  Velvetleaf seed was  planted about 1.5 cm deep using a seed drill either alone or in the interrow area of corn  about 20 cm from the crop row. Granular urea was broadcast at 224 kg N ha-1 after planting. Weed management for species other than velvetleaf consisted of a glyphosate application as a burn-down treatment prior to plant emergence and hand removal for the rest of the season. There was some variability in the density of velvetleaf between plots due to uneven germination, however, in general, velvetleaf density was  about 6 plants m-2 (ranging from 4 to 8 plants m-2) after germination. Treatments were placed in  randomized complete block design with four replicates. Plots were six m long by four rows wide with a row spacing of 76 cm with four replications per treatment.  On June 22nd between 1:00 and 2:00 PM, the apical meristem and all of the young leaves (up to 6 cm in diameter) were collected from 4 individual velvetleaf plants within each treatment plot. The samples from within each plot were pooled and immediately frozen in liquid N¬2 .


title: velvetleaf/corn competition W1RC1B


title: velvetleaf/corn competition C2RW4B


title: F3

tag: B-lymphocyte cell line DNA, maternal grandfather of pedigree XC01423


title: Brain_immunoprecipitated_with_anti-LARK_Biorep1

data_processing: Data generated by MAS5.0 with all default parameters and scaled to a target intensity of 5

molecule: polyA RNA


title: velvetleaf/corn competition C1RW4B

source_name: Velvetleaf/corn competition


title: velvetleaf/corn competition C1RW2B


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish E microarray number FD010_007

status: Public on Dec 05 2006

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

description: Oncorhynchus mykiss 0.75nM TCDD exposed hepatocytes Replicate 4 dye flip

hyb_protocol: Microarray was prepared for hybridization by washing 2 x 5 min with 0.2% SDS, 5 x 1 min with MilliQ water followed by drying using centrifugation (5 min, 514 x g in 50 mL tube). Array was pre-hybridized in 5X SSC, 0.1% SDS, 3% BSA for 1.5 h at 49C, briefly washed 3 X 20 sec in MilliQ water and dried by centrifugation. Labeled cDNAs were hybridized to pre-warmed microarray in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution, and 4 ul of Genisphere LNA dT blocker) for 16 h at 49C. Coverslips were removed in 2X SSC, 0.1% SDS at 49C. The arrays were washed 1 x 10 min at 49C (2X SSC, 0.1% SDS). All subsequent washes were at room temperature; 2 x 5 min in 2X SSC, 0.1% SDS, 2 x 5 min in 1X SSC and 4 x 5 min in 0.1X SSC and dried by centrifugation.

scan_protocol: Fluorescent array images were collected immediately for both Cy3 and Cy5 using ScanArray Express (PerkinElmer).  Image intensity data were extracted using Imagene 5.5 software (Biodiscovery).

data_processing: Only elements deemed present by Imagene software and with control values greater then the average base/proportional value were used.  Expression ratios were generated using background corrected lowess normalized data using GeneSpringGX 7 software (Agilent Technologies, Palo Alto, Ca, USA).

organism: Oncorhynchus mykiss

source_name: Fish E hepatocytes

label_protocol: Labeled cDNA was generated using a SuperScript Indirect cDNA Labeling System kit (Invitrogen) according to the manufacturer's instructions. For each sample 5.0 ug of total RNA was used to generate modified cDNAs.

extract_protocol: Qiagen RNeasy mini kit according to manufacturer's protocol

tag: 0.75nM TCDD exposed

extract_protocol: Qiagen RNeasy mini kit according to manufacturers protocol

tag: 0.1% DMSO Control exposed


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish E microarray number FD010_008

description: Oncorhynchus mykiss 0.75nM TCDD exposed hepatocytes Replicate 4


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish E microarray number FD010_006

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 4

tag: 0.1mM PQ exposed


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish E microarray number FD010_005

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 4 dye flip


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish E microarray number FD009_048

description: Oncorhynchus mykiss 10nM EE2 exposed hepatocytes Replicate 4 dye flip

tag: 10nM EE2 exposed


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish D microarray number FD009_042

description: Oncorhynchus mykiss 0.75nM TCDD exposed hepatocytes Replicate 3 dye flip

source_name: Fish D hepatocytes


title: S73_NG

data_processing: Qspline normalization

label: cyanine 3

tag: single female genomic DNA

label: cyanine 5


title: S80_NG


title: Rainbow trout hepatocycte Mix exposure Fish E microarray number FD009_044

description: Oncorhynchus mykiss Mix exposed hepatocytes Replicate 4 dye flip

tag: Mix exposed


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish D microarray number FD009_036

description: Oncorhynchus mykiss 10nM EE2 exposed hepatocytes Replicate 3 dye flip


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish D microarray number FD009_041

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 3


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish D microarray number FD009_043

description: Oncorhynchus mykiss 0.75nM TCDD exposed hepatocytes Replicate 3


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish D microarray number FD009_040

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 3 dye flip


title: Rainbow trout hepatocycte Mix exposure Fish D microarray number FD009_033

description: Oncorhynchus mykiss Mix exposed hepatocytes Replicate 3


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish E microarray number FD009_050

description: Oncorhynchus mykiss 0.75mM NQO exposed hepatocytes Replicate 4 dye flip

tag: 0.75mM NQO exposed


title: S70_NG

description:
cyanine 3 = sample
cyanine 5 = reference


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish E microarray number FD009_051

description: Oncorhynchus mykiss 0.75mM NQO exposed hepatocytes Replicate 4


title: Rainbow trout hepatocycte Mix exposure Fish D microarray number FD009_032

description: Oncorhynchus mykiss Mix exposed hepatocytes Replicate 3 dye flip


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish D microarray number FD009_038

description: Oncorhynchus mykiss 0.75mM NQO exposed hepatocytes Replicate 3 dye flip


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish D microarray number FD009_039

description: Oncorhynchus mykiss 0.75mM NQO exposed hepatocytes Replicate 3


title: Rainbow trout hepatocycte Mix exposure Fish B microarray number FD009_030b

description: Oncorhynchus mykiss Mix exposed hepatocytes Replicate 2 dye flip

source_name: Fish B hepatocytes


title: S71_NG


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish E microarray number FD009_049

description: Oncorhynchus mykiss 10nM EE2 exposed hepatocytes Replicate 4


title: Rainbow trout hepatocycte Mix exposure Fish E microarray number FD009_045

description: Oncorhynchus mykiss Mix exposed hepatocytes Replicate 4


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish B microarray number FD009_029b

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 2


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish D microarray number FD009_037

description: Oncorhynchus mykiss 10nM EE2 exposed hepatocytes Replicate 3


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish A microarray number FD009_031b

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 1 dye flip

source_name: Fish A hepatocytes


title: Comparative genomic hybridisation of E. coli WK8 (experiment 1)

city: St. Gallen

first: Julian

last: Ihssen

address: Lerchenfeldstrasse 5

country: Switzerland

institute: EMPA

description: Goal of the study was to analyse the prevalence of MG1655 genes in environmental Escherichia coli. The strains were isolated during routine screening of drinking water catchment sites in Switzerland

hyb_protocol: Overnight incubation in sealed boxes in water bath at 42°C. 3 washing steps Procedure as described in the manufacturers protocol (MWG)

scan_protocol: Affimetrix 428 scanner, standard scan protocol for microarray glass slides, appropriate adjustion of gain

data_processing: manual control and correction of spot quantification areas, normalisation of total Cy5 intensity to total Cy3 intensity

organism: Escherichia coli

source_name: reference strain

label_protocol: random hexamer-primed labelling according to the protocol of DeRisi (www.microarrays.org/pdfs/GenomicDNALabel_A.pdf)

extract_protocol: Total genomic DNA was extracted from an LB overnight culture with genomic DNA purification kit (Fermentas GmbH, Germany) according to the manufacturers instructions.

tag: labelled chromosomal DNA of the laboratory strain K-12 MG1655

tag: environmental strain WK8

tag: isolated from source water in the Limmat valley, Switzerland

tag: ECOR group A

tag: biological replicate No. 1 (Cryoculture streaked out, single colony inoculated in LB tube)


title: Comparative genomic hybridisation of E. coli WK8 (experiment 2)


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish A microarray number FD009_026b

description: Oncorhynchus mykiss 0.75nM TCDD exposed hepatocytes Replicate 1 dye flip


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish A microarray number FD009_025b


title: Comparative genomic hybridisation of E. coli WK5 (experiment 1)

tag: environmental strain WK5

tag: isolated from source water in the upper Lake Zurich region, Switzerland


title: Rainbow trout hepatocycte 0.1mM PQ exposure Fish B microarray number FD009_028b

description: Oncorhynchus mykiss 0.1mM PQ exposed hepatocytes Replicate 2 dye flip


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish B microarray number FD009_021b

description: Oncorhynchus mykiss 0.75nM TCDD exposed hepatocytes Replicate 2 dye flip


title: Comparative genomic hybridisation of E. coli WK5 (experiment 2)

tag: isolated from source water in the Linth valley, Switzerland

tag: biological replicate No. 2 (Cryoculture streaked out, single colony inoculated in LB tube)


title: Comparative genomic hybridisation of E. coli WK4 (experiment 2)

tag: environmental strain WK4


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish A microarray number FD009_027b

tag: 0.75nM TCDD exposed


title: Rainbow trout hepatocycte 0.75nM TCDD exposure Fish B microarray number FD009_022b

tag: 0.1% DMSO Control exposed


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish B microarray number FD009_020b

description: Oncorhynchus mykiss 0.75mM NQO exposed hepatocytes Replicate 2 dye flip


title: Comparative genomic hybridisation of E. coli WK3 (experiment 1)

hyb_protocol: Overnight incubation in sealed boxes in water bath at 42°C, 3 washing steps Procedure as described in the manufacturers protocol (MWG)

tag: environmental strain WK3


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish B microarray number FD009_018b

description: Oncorhynchus mykiss 10nM EE2 exposed hepatocytes Replicate 2 dye flip

tag: 10nM EE2 exposed


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish A microarray number FD009_012b

description: Oncorhynchus mykiss 0.75mM NQO exposed hepatocytes Replicate 1 dye flip


title: S72_NG

description:
cyanine 3 = sample
cyanine 5 = reference

tag: single female genomic DNA

tag: single male reference genomic DNA


title: Comparative genomic hybridisation of E. coli WK1 (experiment 2)

description: Goal of the study was to analyse the prevalence of MG1655 genes in environmental Escherichia coli. The strains were isolated during routine screening of drinking water catchment sites

tag: environmental strain WK1

tag: isolated from source water in the Northern Jurassic region, Switzerland


title: Comparative genomic hybridisation E. coli WK3 (experiment 2)

tag: labelled chromosomal DNA of the laboratory strain K-12 MG1655


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish A microarray number FD009_010b

description: Oncorhynchus mykiss 10nM EE2 exposed hepatocytes Replicate 1 dye flip


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish A microarray number FD009_011b

tag: 0.75mM NQO exposed


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish A microarray number FD009_009b


title: Rainbow trout hepatocycte 10nM EE2 exposure Fish B microarray number FD009_017b


title: Comparative genomic hybridisation of E. coli WK4 (experiment 1)

tag: ECOR group A


title: Lmna H222P heterozygous male 7

status: Public on Dec 02 2006

first: antoine

last: Muchir

address: 630W 168th street

department: Medicine

institute: columbia university

description: 10 weeks

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GC-RMA

label: biotin

organism: Mus musculus

source_name: whole heart

label_protocol: standard Affymetrix procedures

extract_protocol: RNA was extracted using Rneasy kit (QIAGEN)


title: Rainbow trout hepatocycte Mix exposure Fish B microarray number FD009_006b

tag: Mix exposed


title: Comparative genomic hybridisation of E. coli WK 1 (experiment 1)

description: Goal of the study was to analysed the prevalence of MG1655 genes in environmental Escherichia coli. The strains were isolated during routine screening of drinking water catchment sites

tag: labelled chromosomal DNA of laboratory strain K-12 MG1655

tag: biological replicate No. 1 (Cryoculture streaked out, single colony inoculated in LB tube)


title: mutant spt15, 5% EtOH, 60 g/L glucose, replicate 1

status: Public on Dec 01 2006

city: Cambridge

first: Joel

last: Moxley

address: 77 Massachusettes Ave

institute: MIT

description: mutant spt15, 5% EtOH, 60 g/L glucose

data_processing: Bioconductor with RMA background correction, qspline normalization, and Li-Wong expression value summaries

organism: Saccharomyces cerevisiae

label_protocol: The extracted RNA was processed by Ambion Services using the Affymetrix protocols with the exception of Ambion ArrayScript substituted for SuperScript and Vivaspin Concentrators substituted for Qiagen cleanup columns.

extract_protocol: Strains were cultured at 30C with 225 rpm orbital shaking in 30 mL YSC -URA medium with the indicated ethanol concentration in 50 mL closed conical tubes.  The cultures harvested at approximately OD 0.4.  Protocols from RAmbion RiboPure Yeast RNA extraction kits were followed.

tag: genetic and environmental variation indicated in Sample_title


title: wild type, 5% EtOH, 60 g/L glucose, replicate 2

description: wild type, 5% EtOH, 60 g/L glucose


title: mutant spt15, 5% EtOH, 60 g/L glucose, replicate 2 (OUTLIER)

description: mutant spt15, 5% EtOH, 60 g/L glucose


title: wild type, 5% EtOH, 60 g/L glucose, replicate 1

description: wild type, 5% EtOH, 60 g/L glucose


title: Rainbow trout hepatocycte 0.75mM NQO exposure Fish B microarray number FD009_019b


title: mutant spt15, 5% EtOH, 60 g/L glucose, replicate 3

description: mutant spt15, 5% EtOH, 60 g/L glucose


title: wild type, 5% EtOH, 60 g/L glucose, replicate 3

description: wild type, 5% EtOH, 60 g/L glucose


title: Rainbow trout hepatocycte Mix exposure Fish A microarray number FD009_002b

description: Oncorhynchus mykiss Mix exposed hepatocytes Replicate 1 dye flip


title: Rainbow trout hepatocycte Mix exposure Fish A microarray number FD009_001b


title: wild type, 0% EtOH, 20 g/L glucose, replicate 3

description: wild type, 0% EtOH, 20 g/L glucose


title: mutant spt15, 0% EtOH, 20 g/L glucose, replicate 1

description: mutant spt15, 0% EtOH, 20 g/L glucose


title: mutant spt15, 0% EtOH, 20 g/L glucose, replicate 3

description: mutant spt15, 0% EtOH, 20 g/L glucose


title: large airways, smoker 020506R, MAS5

status: Public on Nov 21 2006

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: large airways, non-smoker 020506R, MAS5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HuGeneFL. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray 2500.

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.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: M

tag: Ethnic group

value: black

tag: Smoking Status

value: smoker, 20 pack-years

tag: Lung

value: right


title: large airways, smoker 011130R, MAS5

description: large airways, non-smoker 011130R, MAS5

value: F

value: white

value: smoker, 38 pack-years


title: mutant spt15, 0% EtOH, 20 g/L glucose, replicate 2

description: mutant spt15, 0% EtOH, 20 g/L glucose


title: wild type, 0% EtOH, 20 g/L glucose, replicate 1

description: wild type, 0% EtOH, 20 g/L glucose


title: large airways, smoker 020506L, MAS5

description: large airways, non-smoker 020506L, MAS5

value: left


title: wild type, 0% EtOH, 20 g/L glucose, replicate 2

description: wild type, 0% EtOH, 20 g/L glucose


title: large airways, smoker 011024R, MAS5

description: large airways, non-smoker 011024R, MAS5

value: smoker, 19 pack-years


title: EGFP-expressing BM progenitors vs Notch1-IC-expressing BM progenitors

city: Collegeville

first: Tomas

last: Vilimas

state: PA

address: 1250 S. Collegeville Rd.

department: Oncology Discovery Technology Group

institute: GlaxoSmithKline

description: Standard Agilent protocols (carried out by Clinical Data/Icoria/Paradigm Genetics)

data_processing: Agilent Feature Extraction software (carried out by Clinical Data/Icoria/Paradigm Genetics)

label: Cy3 or Cy5 (dye swaps)

source_name: bone marrow lineage-negative progenitors carrying a EGFP retrovirus, 4 days

label_protocol: Clinical Data/Icoria/Paradigm Genetics standard protocols

growth_protocol:
Media: Opti-MEM supplemented with 10% FBS (Sigma), 1% Pen/Strep, 0.1% beta-mercaptoethanol, 50 ng/mL SCF, 50 ng/mL Flt3-L, 25 ng/mL IL-6, 25 ng/mL IL-7.
Culture time: 6 days.
Retroviral infection: day 2, day 4.
Flow-sorting (CD3, CD19, CD11b, DX5, TER119, Gr1 antibodies): day 6.

extract_protocol: RNaqueous Micro columns (Ambion)

treatment_protocol: retroviral infection: standard protocols

tag: strain

tag: sex

value: mixed.

tag: age

value: 4-10 weeks.

tag: isolation of lineage-negative progenitors

value: flow-sorting of femur and tibia bone marrow treated with PE-labeled antibodies against CD3, CD19, CD11b, DX5, TER119, Gr1.

source_name: bone marrow lineage-negative progenitors carrying a Notch1-IC retrovirus, 4 days


title: large airways, smoker 011024L, MAS5

description: large airways, non-smoker 011024L, MAS5


title: large airways, smoker 011130L, MAS5

description: large airways, non-smoker 011130L, MAS5


title: EGFP-expressing BM progenitors vs Notch1-IC-expressing BM progenitors cultured on OP9-DL1 stroma

hyb_protocol: Standard Agilent protocols (carried out by Clinical Data/Icoria/Paradigm Genetics)

label_protocol: Clinical Data/Icoria/Paradigm Genetics standard protocols.

extract_protocol: RNaqueous Micro columns (Ambion).

treatment_protocol: retroviral infection: standard protocols.

source_name: bone marrow lineage-negative progenitors carrying a Notch1-IC retrovirus, cultured on OP9-DL1 stroma

growth_protocol:
Media: Opti-MEM supplemented with 10% FBS (Sigma), 1% Pen/Strep, 0.1% beta-mercaptoethanol, 50 ng/mL SCF, 50 ng/mL Flt3-L, 25 ng/mL IL-6, 25 ng/mL IL-7.
Culture time: 6 days.
Retroviral infection: day 2, day 4.
Flow-sorting (CD3, CD19, CD11b, DX5, TER119, Gr1 antibodies): day 6.
Co-culturing on OP9-DL1 stromal cells: day 6 to day 13 according to standard protocols.


title: large airways, smoker 010814L, MAS5

description: large airways, non-smoker 010814L, MAS5

value: smoker, 28 pack-years


title: large airways, smoker 010808L, MAS5

description: large airways, non-smoker 010808L, MAS5

value: smoker, 8 pack-years


title: large airways, smoker 010809R, MAS5

description: large airways, non-smoker 010809R, MAS5

value: smoker, 14 pack-years


title: large airways, smoker 010618R, MAS5

description: large airways, non-smoker 010618R, MAS5

value: smoker, 10 pack-years


title: large airways, smoker 010809L, MAS5

description: large airways, non-smoker 010809L, MAS5


title: large airways, smoker 010618L, MAS5

description: large airways, non-smoker 010618L, MAS5


title: large airways, smoker 010808R, MAS5

description: large airways, non-smoker 010808R, MAS5


title: large airways, smoker 010228L, MAS5

description: large airways, non-smoker 010228L, MAS5

value: hispanic

value: smoker, 30 pack-years


title: large airways, smoker 010319L, MAS5

description: large airways, non-smoker 010319L, MAS5

value: black


title: large airways, smoker 010509L, MAS5

description: large airways, non-smoker 010509L, MAS5

value: M

value: smoker, 20 pack-years


title: large airways, smoker 010205R, MAS5

description: large airways, non-smoker 010205R, MAS5

value: smoker, 12 pack-years

value: right


title: large airways, smoker 010529R, MAS5

description: large airways, non-smoker 010529R, MAS5

value: white

value: smoker, 15 pack-years


title: large airways, smoker 010814R, MAS5

description: large airways, non-smoker 010814R, MAS5


title: large airways, smoker 010228R, MAS5

description: large airways, non-smoker 010228R, MAS5


title: large airways, smoker 010509R, MAS5

description: large airways, non-smoker 010509R, MAS5


title: large airways, smoker 010529L, MAS5

description: large airways, non-smoker 010529L, MAS5

value: left


title: large airways, smoker 010615L, MAS5

description: large airways, non-smoker 010615L, MAS5

value: smoker, 24 pack-years


title: large airways, smoker 010319R, MAS5

description: large airways, non-smoker 010319R, MAS5

value: F


title: large airways, smoker 010205L, MAS5

description: large airways, non-smoker 010205L, MAS5


title: Met1-6_Hpy/Col_Hpy

status: Public on Nov 26 2006

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Restriction enzyme (HpyCH4 IV) based methylation mapping of the Arabidopsis genome.

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Set MAUI hybridization unit to 42 deg C and allow time for the temperature to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bottom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5 microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microliter Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the NimbleGen arrays. They are required for proper extraction of array data from the scanned image. Mix the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disassembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put the array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sample may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If there are, very gently massage any bubbles to either of the ends, away from the center of the array. Avoid applying too much pressure since this will force liquid out of the ports. Place the loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Close the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm that the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solutions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One dish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works well. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften the adhesive on the hybridization chamber; this will help prevent braking the array. Place the remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I: 225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C. Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not let the surface of the slide dry out at any point during washing. While the chip is submerged, carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfer the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agitation. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wash over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation. Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dark desiccator.

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Axon Scanner (model 4000B). Turn on the power of the scanner. The switch is on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow lasers to warm. Open the scanner door and open the side carriage. Place chip in carriage so that array is face down and barcode end is closest to you. Move the black lever on the left side of the carriage left until the array is lying flat in the carriage. Release the lever so that the arry is pushed over gently to the right side of the carriage and held firmly. Close the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lines to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simultaneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the full arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array image and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side of the screen, click the Scan Area icon. Click and drag to define a box that bounds the visibile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan image. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole image and adjust the brightness and contrast of the displayed image to eliminate visible saturation. Based on the appearance of the array features, adjust the PMT setting as appropriate. The features should be mostly yellow. If your features are mostly green, either decrease the 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 532 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check global intensity of the features. On the top left side of the screen make sure you have the 532 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure the Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the green PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity level (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark.  The histogram only graphs the area of the image that is viewable in the screen on the image tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are properly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the 532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 (ch_635/ch_532) ratios were bi-weight mean centered

organism: Arabidopsis thaliana

source_name: Arabidopsis, ecotype Columbia, 25-day old whole plants without roots

label_protocol: Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol: Methods are described in publication available at http://dx.doi.org/10.1038/ng1929.

tag: Ecotype

value: Columbia, Age:25 days old, Tissue:whole plant

source_name: Arabidopsis, ecotype Col-gl with met1-6 mutation, adult plants

label_protocol: Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

value: met1-6 mutation in the Col-gl background, Age:adult plant, Tissue:whole plant


title: slide48_H

status: Public on Jul 21 2006

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: RNA was isolated from eight to twenty anthers per each individual tassel using Trizol reagent (Invitrogen, Carlbad, CA) as per manufacturer's instructions. Equal amounts of RNA from one to four individuals per stage per floret type (i.e., upper or lower) were pooled randomly to generate one biological replicate. In total, 24 biological replicates (two biological replicates per stage per floret type) were generated. Approximately 100 ng of total RNA from each biological replicate were used as starting material for T7-based linear RNA amplification, performed as described by Nakazono et al. (2003). Each biological replicate yielded between 30 and 50 micrograms of amplified RNA (aRNA). Approximately 3 micrograms of aRNA for each sample was indirectly labeled with Cy dye and hybridized to the GPL3021 sample platform.

hyb_protocol: Fluorescent targets were hybridized as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (48 total) was scanned six times in ascending amounts of laser power and PMT gain with a ScanArray 5000 (Packard, Meriden, CT). Three scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide. The values for the low, medium, and high scan intensity data sets were 5.7, 7.2 and 8.7, respectively.

data_processing: An R implementation of the lowess normalization method (Dudoit and Fridlyand, 2002) was used to normalize the two channels for each combination of slide and scan intensity. The lowess normalized data from each scan was used to conduct a mixed linear model analysis separately for each of 12,160 spots using a strategy similar to that of Wolfinger et al., (2001)

organism: Zea mays

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid/late microspore (mixed) developmental stage by light microscopy

label_protocol: Fluorescent targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Only targets that contained more than 3000 picomoles of cDNA, more than 60 picomoles of Cy dye and more than one dye molecule per 50 bases were used for hybridizations.

extract_protocol: Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer's instructions

tag: Inbred line

value: Ky21;Floret:Upper;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM2u

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the mid/late-microspore (mixed) developmental stage by light microscopy

label_protocol: Fluorescent targets were synthesized and labeled as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Only targets that contained more than 3000 picomoles of cDNA, more than 60 picomoles of Cy dye and more than one dye molecule per 50 bases were used for hybridizations.

value: Ky21;Floret:Lower;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM2L


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 4 h post inoculation	44

status: Public on Nov 29 2007

city: Mountain Grove

first: Wenping

last: Qiu

state: MO

address: 9740 Red Spring Road

department: Agriculture

institute: Missouri State University

description: Gene expression data from V. aestivalis 'Norton ' at 0 hour post inoculation of E. necator conidiospores

hyb_protocol: cRNA was cleaned up by the Affymetrix sample cleanup module which in included in the One-Cycle Target Labeling kit. Fifteen ug of cRNA at concentration of 1.301ug/ul were used for hybridization. Prior to hybridization, cRNA was heated at 94ºC for 35 min, and was fragmented to 35 to 200 nucleotides.  After adding hybridization buffer to the fragmented samples, hybridization cocktails were boiled for 5 min, incubated for 5 min at 45ºC, then centrifuged for 5 minutes prior to loading per standard one-cycle protocol. Hybridization took place in an Affy hybridization oven model 640, for 16h at 45ºC. All washing took place on the fluidics station (as per the recommended fluidics protocol) with non-stringent wash buffer (6X SSPE and 0.01% Tween-20) and Stringent wash buffer (100mM MES, 0.1M NaCl, 0.01% Tween-20). Fluorescence was amplified by first adding streptavidin-phycoerythrin (SAPE) stain, then adding a biotinylated antibody (anti-streptavidin) solution, followed by another SAPE staining (as per standard one-cycle protocol). The fluidics protocol Midi_Euk2v3 was used (as per V. vinifera microarray package insert) on fluidics station model 450.

scan_protocol: Affymetrix Scanner 3000 7G was used to collect at resolution of 1.56um with emission filter at a wavelength of 570nm and excitation wavelength of 532nm.

data_processing: Raw intensity data were processed using the GeneChip Operating Software Version 1.2 (GCOS 1.2; Affymetrix, 2001). Background correction and expression value calculation were performed as described by Affymetrix (2002). Normalization was done by global scaling, with a target intensity value of 150 (Affymetrix, 2001). Probe sets with missing values were deleted across all replicates and species to allow comparisons among datasets

organism: Vitis aestivalis

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 4 hour after inoculation with E. necator conidiospores

label_protocol: The cDNA synthesis and antisense cRNA amplification/biotin labeling was performed using the One-Cycle Target Labeling Kit (Catalog number: 900493, Affymetrix, Santa Clara, California)

growth_protocol: 14 hours day/10 hours night. Light intensity: 500 umol m-2.  Light source: high pressure sodium and metal halide. Temperature: 25°C.  Relative humidity: 85%.

extract_protocol: Total RNA was extracted from each replicate sample individually. The leaves were ground in liquid nitrogen and homogenized in extraction buffer (2% Hexadecyltrimethyl Ammonium Bromide 1%  sodium dodecyl sulfate, 2.5M NaCl, 0.5M Tris, 50mM EDTA, 5% beta-mercaptoethanol, and 3% polyvinyl poly-pyrrolidone. Following a 30-min incubation at -80°C, the samples were thawed and centrifuged. The supernatant was supplemented with 1/30 volume of 3 M sodium acetate (pH5.2) and 1/10 volume of ethanol, incubated on ice and centrifuged three times at 7000g, 30 min 4 ºC, each time transferring the supernatant into a clean tube. The supernatant was supplemented with 1/9 volume of 3 M sodium acetate (pH5.2) and iso-propanol to a final concentration of 33%. Following 60-min incubation at -20°C, the RNA was collected by centrifugation at 12,000g, 30 min, 4 ºC. The RNA was then supplemented with 1/3 volume of 8 M LiCl and incubated overnight at 4 °C. RNA was then collected by centrifugation at 12,000g, 30 min, 4 ºC, washed with 75% ethanol, and resuspended in 40 ul DEPC water.  Ten micrograms of total RNA were treated with Turbo DNase I (Ambion) and purified with RNA purification kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: third or forth leaves were inocualted with E. necator conidiospores by touching 10 day-old powdery mildew colonies directly onto the target leaves

tag: Fully-expanded leaves at the third or fourth position from the top of each shoot were used for treatment


title: ein5-1 cordycepin 17-6

status: Public on Jul 26 2006

city: La Jolla

first: Joseph

middle: R.

last: Ecker

state: CA

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

description: For the oligonucleotide tiling array experiments 10 days-old light-grown Arabidopsis ein5-1 seedlings were transferred to a Petri-plate containing incubation buffer (1mM Pipes, 1mM sodium citrate, 1mM KCl, 15mM sucrose), and maintained in agitation at 75 rpm for 30 min covered with foil. At this point vacuum was applied for exactly 15 seconds and cordycepin (Sigma Chemical Co., St. Louis) was added to a final concentration of 150 ug/ml. The seedlings were then incubated for 2 more hours in the dark at room temperature and kept in agitation at 75 rpm in Petri-plates. The seedlings were then briefly blotted to on filter paper to dry and kept in liquid nitrogen. Total RNA was extracted from the samples using the RNAeasy plant kit (Qiagen, Valencia, CA). Biotinylated target RNA was prepared from 120 ug of total RNA from each sample using the GeneChip® Expression Analysis system (Affymetrix, Santa Clara, CA). Each sample of the purified and fragmented labeled target cRNA was hybridized to one set of Arabidopsis genome tiling arrays consisting of twelve custom made arrays (Yamada, K et al., 2003). Hybridization, washes and the staining were carried out as described above for the Affymetrix array ATH1. Cell files were obtained using the GCOS software (Affymetrix, Santa Clara, CA) and the ChipViewer software was used to visualize and analyze the tiling chip data (Yamada et al. 2003.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome.  Science 302, 842-846). Data submitted by Huaming Chen. Contributors: Gabriela Olmedo, Hongwei Guo, Brian D. Gregory, Saeid D. Nourizadeh, Laura Aguilar-Henonin, Hongjiang Li, Fengying An, Plinio Guzman, and Joseph R. Ecker

hyb_protocol: Each sample of the purified and fragmented labeled target cRNA was hybridized to one set of Arabidopsis genome tiling arraysconsisting of twelve custom made arrays (Yamada, K et al., 2003). Hybridization, washes and the staining were carried out as described above for the Affymetrix array ATH1.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: CEL files were obtained using the GCOS software (Affymetrix, Santa Clara, CA) and the ChipViewer software was used to visualize and analyze the tiling chip data (Yamada et al. 2003.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome.  Science 302, 842-846).

label: Biotinylated

growth_protocol: 10 days-old light-grown


title: slide48_M


title: Col-0 cordycepin 17-rc-6

description: For the oligonucleotide tiling array experiments 10 days-old light-grown Arabidopsis Col-0 seedlings were transferred to a Petri-plate containing incubation buffer (1mM Pipes, 1mM sodium citrate, 1mM KCl, 15mM sucrose), and maintained in agitation at 75 rpm for 30 min covered with foil. At this point vacuum was applied for exactly 15 seconds and cordycepin (Sigma Chemical Co., St. Louis) was added to a final concentration of 150 ug/ml. The seedlings were then incubated for 2 more hours in the dark at room temperature and kept in agitation at 75 rpm in Petri-plates. The seedlings were then briefly blotted to on filter paper to dry and kept in liquid nitrogen. Total RNA was extracted from the samples using the RNAeasy plant kit (Qiagen, Valencia, CA). Biotinylated target RNA was prepared from 120 ug of total RNA from each sample using the GeneChip® Expression Analysis system (Affymetrix, Santa Clara, CA). Each sample of the purified and fragmented labeled target cRNA was hybridized to one set of Arabidopsis genome tiling arrays consisting of twelve custom made arrays (Yamada, K et al., 2003). Hybridization, washes and the staining were carried out as described above for the Affymetrix array ATH1. Cell files were obtained using the GCOS software (Affymetrix, Santa Clara, CA) and the ChipViewer software was used to visualize and analyze the tiling chip data (Yamada et al. 2003.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome.  Science 302, 842-846). Data submitted by Huaming Chen. Contributors: Gabriela Olmedo, Hongwei Guo, Brian D. Gregory, Saeid D. Nourizadeh, Laura Aguilar-Henonin, Hongjiang Li, Fengying An, Plinio Guzman, and Joseph R. Ecker


title: slide47_H

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid-microspore developmental stage by light microscopy

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the mid-microspore developmental stage by light microscopy


title: slide48_L


title: slide47_M


title: Col-0 cordycepin 17-6

label_protocol: Total RNA was extracted from the samples using the RNAeasy plant kit (Qiagen, Valencia, CA). Biotinylated target RNA was prepared from 120 ug of total RNA from each sample using the GeneChip® Expression Analysis system (Affymetrix, Santa Clara, CA).

treatment_protocol: 10 days-old light-grown Arabidopsis Col-0 seedlings were transferred to a Petri-plate containing incubation buffer (1mM Pipes, 1mM sodium citrate, 1mM KCl, 15mM sucrose), and maintained in agitation at 75 rpm for 30 min covered with foil. At this point vacuum was applied for exactly 15 seconds and cordycepin (Sigma Chemical Co., St. Louis) was added to a final concentration of 150 ug/ml. The seedlings were then incubated for 2 more hours in the dark at room temperature and kept in agitation at 75 rpm in Petri-plates. The seedlings were then briefly blotted to on filter paper to dry and kept in liquid nitrogen.


title: Col-0 cordycepin 17-5

source_name: 10 days-old light-grown Arabidopsis Col-0 seedlings

extract_protocol: Total RNA was extracted from the samples using the RNAeasy plant kit (Qiagen, Valencia, CA).


title: ein5-1 cordycepin 17-1

treatment_protocol: 10 days-old light-grown Arabidopsis ein5-1 seedlings were transferred to a Petri-plate containing incubation buffer (1mM Pipes, 1mM sodium citrate, 1mM KCl, 15mM sucrose), and maintained in agitation at 75 rpm for 30 min covered with foil. At this point vacuum was applied for exactly 15 seconds and cordycepin (Sigma Chemical Co., St. Louis) was added to a final concentration of 150 ug/ml. The seedlings were then incubated for 2 more hours in the dark at room temperature and kept in agitation at 75 rpm in Petri-plates. The seedlings were then briefly blotted to on filter paper to dry and kept in liquid nitrogen.


title: Col-0 cordycepin 17-3


title: ein5-1 cordycepin 17-rc-6

source_name: 10 days-old light-grown Arabidopsis ein5-1 seedlings


title: Col-0 cordycepin 17-rc-1


title: ein5-1 cordycepin 17-2


title: Col-0 cordycepin 17-rc-5


title: Col-0 cordycepin 17-rc-4


title: ein5-1 cordycepin 17-5


title: ein5-1 cordycepin 17-rc-5


title: Col-0 cordycepin 17-1


title: slide46_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the early microspore developmental stage by light microscopy

value: Ky21;Floret:Upper;Developmental stage:Early microspore;Sample name:EM2u

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the early microspore developmental stage by light microscopy

value: Ky21;Floret:Lower;Developmental stage:Early microspore;Sample name:EM2L


title: slide47_L


title: Col-0 cordycepin 17-rc-2


title: ein5-1 cordycepin 17-rc-3


title: Notch1-IC-expressing BM progenitors vs Notch1-IC-expressing BM progenitors cultured on OP9-DL1 stroma

scan_protocol: Standard Agilent protocols (carried out by Clinical Data/Icoria/Paradigm Genetics)

value: mixed.

value: 4-10 weeks.

value: flow-sorting of femur and tibia bone marrow treated with PE-labeled antibodies against CD3, CD19, CD11b, DX5, TER119, Gr1.


title: slide46_H


title: slide46_L


title: slide45_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the tetrad developmental stage by light microscopy

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the tetrad developmental stage by light microscopy


title: ein5-1 cordycepin 17-rc-4


title: slide44_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the dyad/tetrad (mixed) developmental stage by light microscopy

value: Ky21;Floret:Upper;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T2u

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the dyad/tetrad (mixed) developmental stage by light microscopy

value: Ky21;Floret:Lower;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T2L


title: ein5-1 cordycepin 17-rc-2


title: slide44_L


title: slide44_H


title: ein5-1 cordycepin 17-rc-1


title: slide45_L


title: ein5-1 cordycepin 17-4


title: Col-0 cordycepin 17-2


title: slide43_H

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the meiocyte developmental stage by light microscopy

source_name: Anthers dissected from the lower floret of spikelets from maize tassels and staged at the meiocyte developmental stage by light microscopy


title: ein5-1 cordycepin 17-3


title: slide43_L


title: slide18_M

source_name: Anthers dissected from the upper floret of spikelets from maize tassels and staged at the mid/late-microspore (mixed) developmental stage by light microscopy

value: Ky21;Floret:Upper;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM1u

value: Ky21;Floret:Lower;Developmental stage:Mid/late-microspore (mixed);Sample name:M/LM1L


title: slide17_M


title: slide15_L


title: Col-0 cordycepin 17-4


title: slide18_L


title: slide17_L


title: slide18_H


title: slide16_H

value: Ky21;Floret:Upper;Developmental stage:Early microspore;Sample name:EM1u

value: Ky21;Floret:Lower;Developmental stage:Early microspore;Sample name:EM1L


title: slide45_H


title: slide16_L


title: slide15_H


title: slide16_M


title: Col-0 cordycepin 17-rc-3


title: slide17_H


title: slide14_H

value: Ky21;Floret:Upper;Developmental stage:Dyad/Tetrad (mixed);Sample name:D/T1u

value: Ky21;Floret:Lower;Developmental stage:Dyad/tetrad (mixed);Sample name:D/T1L


title: slide15_M


title: slide13_M


title: slide14_L


title: slide14_M


title: EC18n186 RpoH 20 min Time course 3

status: Public on Mar 06 2006

city: San Francisco

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

description: Wild type vs RpoH (Sigma 32) 20 min after overexpression

hyb_protocol: cDNA from 16 ug total RNA, 15 ug poly(dI-dC), 3xSSC, 25 mM Hepes (pH7), 0.225% SDS. Samples hybridized on array under a lifterslip for 12 hrs at 65 degrees C

scan_protocol: Slides scanned using GenePix 4000B scanner (Axon). TIFF images analyzed using GENEPIX 3.0 software (Axon).

data_processing: Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot

source_name: Wild type control (20 min)

label_protocol: Indirect labeling method as described in Khodursky et al (2003; Methods Mol Biol 224:61-78)

growth_protocol: M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm

extract_protocol: Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA).

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction

tag: MG1655 PhtpG::lacZ delta lacX74/ptrc99A (control vector)

source_name: RpoH induced (20 min)

tag: MG1655 PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)


title: EC18n122 RpoH 10 min Time course 4

description: Wild type vs RpoH (Sigma 32) 10 min after overexpression

source_name: Wild type control (10 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 10 min after induction

source_name: RpoH induced (10 min)


title: slide13_H


title: slide13_L


title: EC18n171 RpoH 20 min Time course 2


title: EC18n182 RpoH 0 min Time course 3

description: Wild type vs RpoH (Sigma 32) 0 min after overexpression

source_name: Wild type control (0 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 0 min after induction

source_name: RpoH induced (0 min)


title: EC18n183 RpoH 2.5 min Time course 3

description: Wild type vs RpoH (Sigma 32) 2.5 min after overexpression

source_name: Wild type control (2.5 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 2.5 min after induction

source_name: RpoH induced (2.5 min)


title: EC18n181 RpoH 20 min Time course 1


title: EC18n168 RpoH 2.5 min Time course 2


title: EC18n180 RpoH 10 min Time course 1


title: EC18n179 RpoH 5 min Time course 1

description: Wild type vs RpoH (Sigma 32) 5 min after overexpression

source_name: Wild type control (5 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 5 min after induction

source_name: RpoH induced (5 min)


title: EC18n184 RpoH 5 min Time course 3


title: EC18n169 RpoH 5 min Time course 2


title: slide43_M


title: EC18n167 RpoH 0 min Time course 2


title: EC18n185 RpoH 10 min Time course 3


title: EC18n178 RpoH 2.5 min Time course 1


title: CB +/- 3, chip HG-U133A

status: Public on Jan 17 2006

city: Ottawa

first: Theodore

last: Perkins

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E43
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=43
SCGP Sample ID:				S123
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=43#SAMPLE_91
Short description:			Amplified RNA from cord blood.
Estimated purity:				> 98%
RNA concentration:			375 ng/ul
Num cells for RNA prep:			200,000
Sample volume:				40.0 ul

hyb_protocol: Affy

scan_protocol: Affy

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

source_name: Hematopoietic stem and progenitor cells, Cord blood

label_protocol: Affy

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			1. Ficoll separation to isolate mononuclear cells (MNCs)., 2. Lineage depleted cocktail to enrich progenitors (Lin- population).</p> 3. CD34, CD38 and 7AAD fluorochromes to enrich live hematopoietic stem cells using FACS-Vantage.
Method for estimating purity:		Purity was checked after sorting the cells on FACS-Vantage.

treatment_protocol: Assays to confirm viability:		7AAD staining

tag: Defining markers:				Lin-, CD34+, CD38-


title: EC18n177 RpoH 0 min Time course 1


title: CB +/- 3, chip HG-U133B


title: CB +/- 1, chip HG-U133B


title: CB +/- 2, chip HG-U133B


title: CB +/- 1, chip HG-U133A


title: CB +/- 2, chip HG-U133A


title: EC18n170 RpoH 10 min Time course 2


title: Mening SWB WB SW 12b

status: Public on Dec 30 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20553.gif
Infection: Y
name: 20553_Infection

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: Common Reference 2 round amplification 2 ug

source_name: Mening SWB WB SW 12b

tag: Mening SWB WB SW 12b


title: Mening UNSTIM WB SW 12a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20554.gif
Infection: N
name: 20554_Infection

tag: Common Reference 2 round amplification 2 ug

source_name: Mening UNSTIM WB SW 12a

tag: Mening UNSTIM WB SW 12a


title: Mening UNSTIM WB NP 0b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23207.gif
Infection: N
name: 23207_Infection

source_name: Mening UNSTIM WB NP 0b

tag: Mening UNSTIM WB NP 0b


title: Mening UNSTIM WB SW 12b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20570.gif
Infection: N
name: 20570_Infection

source_name: Mening UNSTIM WB SW 12b

tag: Mening UNSTIM WB SW 12b


title: Mening SWB WB SW 12a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20550.gif
Infection: Y
name: 20550_Infection

source_name: Mening SWB WB SW 12a

tag: Mening SWB WB SW 12a


title: Mening UNSTIM WB SW 24b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20530.gif
Infection: N
name: 20530_Infection

source_name: Mening UNSTIM WB SW 24b

tag: Mening UNSTIM WB SW 24b


title: Mening SWB WB NP 1a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20587.gif
Infection: Y
name: 20587_Infection

source_name: Mening SWB WB NP 1a

tag: Mening SWB WB NP 1a


title: Mening UNSTIM WB NP 1a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20588.gif
Infection: N
name: 20588_Infection

source_name: Mening UNSTIM WB NP 1a

tag: Mening UNSTIM WB NP 1a


title: Mening SWB WB NP 6a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20581.gif
Infection: Y
name: 20581_Infection

source_name: Mening SWB WB NP 6a

tag: Mening SWB WB NP 6a


title: Mening SWB WB SW 6b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20566.gif
Infection: Y
name: 20566_Infection

source_name: Mening SWB WB SW 6b

tag: Mening SWB WB SW 6b


title: Mening UNSTIM WB NP 12b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20561.gif
Infection: N
name: 20561_Infection

source_name: Mening UNSTIM WB NP 12b

tag: Mening UNSTIM WB NP 12b


title: Mening UNSTIM WB NP 6b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20584.gif
Infection: N
name: 20584_Infection

source_name: Mening UNSTIM WB NP 6b

tag: Mening UNSTIM WB NP 6b


title: Mening SWB WB NP 1b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20598.gif
Infection: Y
name: 20598_Infection

source_name: Mening SWB WB NP 1b

tag: Mening SWB WB NP 1b


title: Mening SWB WB NP 24b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20548.gif
Infection: Y
name: 20548_Infection

source_name: Mening SWB WB NP 24b

tag: Mening SWB WB NP 24b


title: Mening UNSTIM WB NP 1b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20589.gif
Infection: N
name: 20589_Infection

source_name: Mening UNSTIM WB NP 1b

tag: Mening UNSTIM WB NP 1b


title: Mening UNSTIM WB SW 0a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20546.gif
Infection: N
name: 20546_Infection

source_name: Mening UNSTIM WB SW 0a

tag: Mening UNSTIM WB SW 0a


title: Mening SWB WB NP 24a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20563.gif
Infection: Y
name: 20563_Infection

source_name: Common Reference 2 round amplification 2 ug

source_name: Mening SWB WB NP 24a

tag: Mening SWB WB NP 24a