title: 2-CH-1-1-10

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

source_name: Helianthus annuus control leaf two-week seedlings rep. 1


title: 2-SH-1-1-16

status: Public on Jan 29 2008

type: RNA

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

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

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

molecule: total RNA

organism: Helianthus annuus

source_name: Helianthus annuus two-week old seedlings watered with 150 mM salt solution for up to 9 hours, rep. 1 (leaves)

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

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

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


title: 2-SH-1-1-17


title: 2-CH-1-1-13

source_name: Helianthus annuus control leaf two-week seedlings rep. 2

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


title: 2-CH-1-1-11


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

city: Ithaca

first: Lyza

middle: G

last: Maron

state: NY

address: Tower Rd., Cornell University

department: USDA - ARS

country: USA

institute: Robert W. Holley Center for Agriculture and Health

description:
Cohybridized with GSM260474

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

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

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

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

organism: Zea mays

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

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

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

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

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

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


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

description:
Cohybridized with GSM260479

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

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


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

description:
Cohybridized with GSM260475

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

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


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

description:
Cohybridized with GSM260472

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


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

description:
Cohybridized with GSM260473

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


title: 2-CH-1-1-12


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

description:
Cohybridized with GSM260478

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

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


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

description:
Cohybridized with GSM260470

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

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


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

description:
Cohybridized with GSM260468

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

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


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

description:
Cohybridized with GSM260471

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


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

description:
Cohybridized with GSM260477

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


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

description:
Cohybridized with GSM260476

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


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

description:
Cohybridized with GSM260464

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

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


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

description:
Cohybridized with GSM260462

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


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

description:
Cohybridized with GSM260467

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


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

description:
Cohybridized with GSM260469

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


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

description:
Cohybridized with GSM260466

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

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


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

description:
Cohybridized with GSM260463

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


title: 2-SH-1-1-18

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

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


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

description:
Cohybridized with GSM260465

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


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

description:
Cohybridized with GSM260461

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


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

description:
Cohybridized with GSM260458

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


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

description:
Cohybridized with GSM260460

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


title: Patient 15, Post-Sirolimus

type: genomic

city: Phoenix

first: Kevin

last: Brown

state: AZ

address: 445 N. Fifth Street

institute: TGen

hyb_protocol: Cy5 and Cy3 reactions were combined and hybridized in a total volume of 500 uL with 50 uL human Cot-1 DNA (1 mg/mL; Invitrogen), 25 uL yeast tRNA (5 ug/uL; Sigma-Aldrich, St. Louis, Missouri), 50 uL 10X Control Targets (Agilent), and 250 uL 2X Hybridization Buffer (Agilent). Probe mixtures were denatured via boiling 3 minutes, followed by pre-incubation at 37C for 30 minutes. Probes were added to arrays and arrays were hybridized in a rotating oven (Agilent) at 65C for 48 hours at 10 RPM. Arrays were washed for 5 minutes in CGH Wash Buffer 1 (0.5X SSPE, 0.005% NLauroylsarcosine) at room temperature, 12 minutes in CGH Wash 2 (0.1X SSPE, 0.005% NLauroylsarcosine) at 37C, and 1 minute in Stabilization and Drying Solution (Agilent) at room temperature.

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner at 10 micron resolution.

data_processing: Data was extracted using Agilent Feature Extraction Software v9.1.1 using default CGH extraction parameters (Agilent Protocol CGH-v4_91).

molecule: genomic DNA

organism: Homo sapiens

source_name: Glioma biopsy, Patient 15, Post-Sirolimus

label_protocol:
800 ng tumor DNA or normal female control DNA (Promega, Madison, Wisconsin) was digested with 1 uL AluI (10U/uL; Invitrogen, Carlsbad,
CA) and 1 uL Rsa I (10U/uL; Invitrogen) in 13.33 uL total volume at 37C for 2 hours, followed by heat inactivation at 65C for 10 minutes. Digestion was subsequently verified via agarose gel. DNA samples were labeled using the Bioprime CGH kit (Invitrogen): 13 uL of each digestion was combined with 20 uL 2.5X random primers and incubated at 99C for 5 minutes. Reactions were subsequently snap-cooled on ice. 5 uL Cy5-dUTP (tumor) or Cy3-dUTP (control) (GE Healthcare) was added along with 1 uL Exo-Klenow; reactions were mixed an incubated at 37C for 2 hours. Reactions were stopped with 5 uL stop buffer and cleaned over a Vivaspin 500 column (Sartorious Goettingen, Germany).

extract_protocol: Tumor cell DNA was isolated from microdissected fresh frozen clinical tumor samples using the Qiagen DNeasy Kit (Qiagen, Valencia, California).

tag: 'Patient Number

value: 15', 'Age:55', 'Gender:M', 'KPS:90', 'Rapamycin Dose (mg):10', 'Pre-Op Therapy (days):5', 'Recurrence Number:2', 'Decadron:No', 'EIAED:No', 'Previous Therapies:XRT,T,A, AEE', 'TTP:55'

source_name: Normal Female DNA

extract_protocol: Procured from Promega, Inc.

tag: 'Gender

value: female'


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

description:
Cohybridized with GSM260452

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


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

description:
Cohybridized with GSM260455

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


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

description:
Cohybridized with GSM260459

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


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

description:
Cohybridized with GSM260457

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


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

description:
Cohybridized with GSM260454

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


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

description:
Cohybridized with GSM260456

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


title: Patient 12, Post-Sirolimus

source_name: Glioma biopsy, Patient 12, Post-Sirolimus

value: 12', 'Age:44', 'Gender:F', 'KPS:80', 'Rapamycin Dose (mg):10', 'Pre-Op Therapy (days):8', 'Recurrence Number:4', 'Decadron:Increasing', 'EIAED:Yes', 'Previous Therapies:XRT,T,A, D, I,  L', 'TTP:98'


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

description:
Cohybridized with GSM260453

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


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

description:
Cohybridized with GSM260450

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


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

description:
Cohybridized with GSM260451

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


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

description:
Cohybridized with GSM260448

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


title: Patient 13, Post-Sirolimus

source_name: Glioma biopsy, Patient 13, Post-Sirolimus

value: 13', 'Age:59', 'Gender:M', 'KPS:90', 'Rapamycin Dose (mg):10', 'Pre-Op Therapy (days):5', 'Recurrence Number:2', 'Decadron:Decreasing', 'EIAED:No', 'Previous Therapies:XRT,T,A, I,  L', 'TTP:146'


title: Patient 12, Pre-Sirolimus

source_name: Glioma biopsy, Patient 12, Pre-Sirolimus


title: Patient 5, Post-Sirolimus

source_name: Glioma biopsy, Patient 5, Post-Sirolimus

value: 5', 'Age:47', 'Gender:M', 'KPS:90', 'Rapamycin Dose (mg):5', 'Pre-Op Therapy (days):7', 'Recurrence Number:2', 'Decadron:No', 'EIAED:No', 'Previous Therapies:XRT,T,A, E', 'TTP:42'


title: Patient 9, Post-Sirolimus

source_name: Glioma biopsy, Patient 1, Post-Sirolimus

value: 9', 'Age:61', 'Gender:F', 'KPS:90', 'Rapamycin Dose (mg):10', 'Pre-Op Therapy (days):7', 'Recurrence Number:1', 'Decadron:No', 'EIAED:No', 'Previous Therapies:XRT,T', 'TTP:125'


title: Patient 10, Post-Sirolimus

source_name: Glioma biopsy, Patient 10, Post-Sirolimus

value: 10', 'Age:51', 'Gender:M', 'KPS:90', 'Rapamycin Dose (mg):10', 'Pre-Op Therapy (days):5', 'Recurrence Number:2', 'Decadron:Decreasing', 'EIAED:No', 'Previous Therapies:XRT,T,A, L', 'TTP:39'


title: Patient 6, Post-Sirolimus

source_name: Glioma biopsy, Patient 6, Post-Sirolimus

value: 6', 'Age:74', 'Gender:M', 'KPS:90', 'Rapamycin Dose (mg):5', 'Pre-Op Therapy (days):3', 'Recurrence Number:1', 'Decadron:Decreasing', 'EIAED:No', 'Previous Therapies:XRT,T,A', 'TTP:194'


title: S103_biorep3

city: Stillwater

first: Patricia

middle: J

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

description: Normalized (global median) ratio values obtained for each probe were averaged across replicates. Significant differences were defined as those displaying an average expression fold change greater than 2-fold (log (base 2) ratio ≥ 1.0).

hyb_protocol: Labeled total RNA (1 µg) was hybridized to the microarrays using the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions. Post-hybridization washes were done according to the manufacturer’s (Genisphere) instructions.

scan_protocol: Hybridization signals were measured using a ScanArray Express (PerkinElmer, Boston, MA, USA) and the images where processed using GenePix Pro version 4.0 (Axon, Union City, CA, USA).

data_processing: normalization of log2 ratios using global median normalization

label: Alexa Fluor 647

organism: Ovis aries

source_name: infected animal 103

label_protocol: One µg total RNA was labeled using the 3DNA Array900MPX kit with Alexa Fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random and oligo-dT primes, Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions.

growth_protocol: one-month old lambs from an experimental flock without a known history of contact with ticks and tick-borne pathogens were weaned and left uninfected to serve as controls or infected with a pool of blood samples obtained from commercial flocks with a previous history of TBF, located in the Basque Country, Northern Spain.

extract_protocol: Total RNA was isolated from Buffy coat samples of experimentally infected and control sheep using TriReagent (Sigma, St. Louis, MO, USA) according to manufacturer’s instructions. The RNA was checked using the Experion™ Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA) to evaluate the quality and integrity of RNA preparations.

treatment_protocol: A. phagocytophilum infection was assessed by microscopy and PCR in daily blood samples until 21 days post-infection (dpi). Buffy coat samples were collected from two lambs experimentally infected with A. phagocytophilum.

tag: infected animal 103

label: Alexa Fluor 546

source_name: uninfected animal 103u

treatment_protocol: Lack of A. phagocytophilum infection was assessed by microscopy and PCR in daily blood samples until 21 days. Buffy coat samples were collected from uninfected lambs.

tag: uninfected animal 103u


title: S102_biorep2

source_name: infected animal 102

tag: infected animal 102

source_name: uninfected animal 102u

tag: uninfected animal 102u


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

description:
Cohybridized with GSM260449

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


title: Patient 4, Post-Sirolimus

source_name: Glioma biopsy, Patient 4, Post-Sirolimus

value: 4', 'Age:39', 'Gender:M', 'KPS:80', 'Rapamycin Dose (mg):5', 'Pre-Op Therapy (days):11', 'Recurrence Number:3', 'Decadron:Decreasing', 'EIAED:No', 'Previous Therapies:XRT,T,D,A, E', 'TTP:153'


title: Patient 3, Pre-Sirolimus

source_name: Glioma biopsy, Patient 3, Pre-Sirolimus

value: 3', 'Age:65', 'Gender:M', 'KPS:80', 'Rapamycin Dose (mg):2', 'Pre-Op Therapy (days):7', 'Recurrence Number:3', 'Decadron:Decreasing', 'EIAED:No', 'Previous Therapies:XRT,T,A, Z, C', 'TTP:70'


title: Patient 2, Post-Sirolimus

source_name: Glioma biopsy, Patient 2, Post-Sirolimus

value: 2', 'Age:70', 'Gender:F', 'KPS:80', 'Rapamycin Dose (mg):2', 'Pre-Op Therapy (days):6', 'Recurrence Number:2', 'Decadron:No', 'EIAED:No', 'Previous Therapies:XRT,T,L', 'TTP:40'


title: Patient 1, Post-Sirolimus

label_protocol:
800 ng tumor DNA or normal male control DNA (Promega, Madison, Wisconsin) was digested with 1 uL AluI (10U/uL; Invitrogen, Carlsbad,
CA) and 1 uL Rsa I (10U/uL; Invitrogen) in 13.33 uL total volume at 37C for 2 hours, followed by heat inactivation at 65C for 10 minutes. Digestion was subsequently verified via agarose gel. DNA samples were labeled using the Bioprime CGH kit (Invitrogen): 13 uL of each digestion was combined with 20 uL 2.5X random primers and incubated at 99C for 5 minutes. Reactions were subsequently snap-cooled on ice. 5 uL Cy5-dUTP (tumor) or Cy3-dUTP (control) (GE Healthcare) was added along with 1 uL Exo-Klenow; reactions were mixed an incubated at 37C for 2 hours. Reactions were stopped with 5 uL stop buffer and cleaned over a Vivaspin 500 column (Sartorious Goettingen, Germany).

value: 1', 'Age:46', 'Gender:M', 'KPS:100', 'Rapamycin Dose (mg):2', 'Pre-Op Therapy (days):6', 'Recurrence Number:1', 'Decadron:No', 'EIAED:No', 'Previous Therapies:XRT,T,A', 'TTP:62'

value: Female'


title: Patient 1, Pre-Sirolimus

source_name: Glioma biopsy, Patient 1, Pre-Sirolimus


title: W22 11-day seedling aerial tissue biological replicate 3

status: Public on Jan 26 2008

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: refer to PMID: 16702414

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: MAS5.0 values are reported; the .cel file is also available

label: biotin

source_name: Zea mays 11-day seedling aerial tissue genotype W22

label_protocol: Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).

growth_protocol: Seeds for maize inbreds and hybrids were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 30ºC and night temperature of 22ºC) and sampled between 8:00 and 9:00 am.  The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected.  Each biological replicate consisted of pooled tissue from eight different seedlings of the same genotype.  The sampled tissues were flash frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.

extract_protocol: Total RNA samples were isolated using TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy system (QIAGEN, Valencia, CA).

tag: Genotype

value: W22; Stage:11-day old seedling, all aerial tissue


title: Patient 3, Post-Sirolimus

source_name: Glioma biopsy, Patient 3, Post-Sirolimus

source_name: Normal Female DNA


title: W22 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: B14a 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B14a

value: B14a; Stage:11-day old seedling, all aerial tissue


title: Wf9 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Wf9

value: Wf9; Stage:11-day old seedling, all aerial tissue


title: Wf9 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: Wf9 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: Patient 8, Post-Sirolimus

source_name: Glioma biopsy, Patient 8, Post-Sirolimus

value: 8', 'Age:49', 'Gender:F', 'KPS:90', 'Rapamycin Dose (mg):5', 'Pre-Op Therapy (days):25', 'Recurrence Number:1', 'Decadron:Stable', 'EIAED:No', 'Previous Therapies:XRT,T,A', 'TTP:144'


title: W22 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: B14a 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: MCF10A E2F3 1

status: Public on Jan 28 2008

city: Stanford

first: David

last: Wong

state: CA

address: 269 Campus Drive

institute: Stanford University

description:
Simple annotation: Cell-line, Breast
Image: http://jdemeter-smd-banjo.stanford.edu:8000/MicroArray/gifs/2007-08/76296.gif
Cell Line: E2F3

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 400, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.78; Parameter Scan Time = 11:37:34; Parameter PMT Volts = 550; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 33715; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.78; Parameter Scan Time = 11:37:34; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 277460; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

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: universal reference

label_protocol: not provided

extract_protocol: not provided

tag: universal reference

source_name: MCF10A E2F3 1

tag: MCF10A E2F3 1


title: MCF10A CSN5

description:
Simple annotation: Cell-line, Breast
Image: http://jdemeter-smd-banjo.stanford.edu:8000/MicroArray/gifs/2007-08/76294.gif
Cell Line: CSN5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 320, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 12:10:16; Parameter PMT Volts = 520; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 33746; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 12:10:16; Parameter PMT Volts = 720; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 277491; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: MCF10A CSN5

tag: MCF10A CSN5


title: MCF10A MYC

description:
Simple annotation: Cell-line, Breast
Image: http://jdemeter-smd-banjo.stanford.edu:8000/MicroArray/gifs/2007-08/76293.gif
Cell Line: MYC

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 200, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.23; Parameter Scan Time = 11:59:42; Parameter PMT Volts = 520; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 33736; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.23; Parameter Scan Time = 11:59:42; Parameter PMT Volts = 680; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 277481; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: MCF10A MYC

tag: MCF10A MYC


title: B14a 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: Oh43 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43

value: Oh43; Stage:11-day old seedling, all aerial tissue


title: Oh43xMo17 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43xMo17

value: Oh43xMo17; Stage:11-day old seedling, all aerial tissue


title: Oh43xB73 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43xB73

value: Oh43xB73; Stage:11-day old seedling, all aerial tissue


title: CS H3K9me2/total

city: Seattle

first: Barbara

last: Wakimoto

state: WA

address: University of Washington, Box 351800

department: Biology

institute: University of Washington

description: ChIP and reference DNA samples were amplified using the ligation-mediated PCR method prior to labeling.

hyb_protocol: Hybridization was performed by NimbleGen Systems, Inc. using the standard protocol more information may be found at the Nimblegen website

scan_protocol: Scanning was performed by NimbleGen Systems, Inc. using the standard protocol more information may be found at the Nimblegen website

data_processing: ChIP/reference signal ratios were calculated from the raw signal intensities and normalized by the median of the entire array

organism: Drosophila melanogaster

label_protocol:
Sample labeling was performed by NimbleGen Systems, Inc. using the standard random-priming protocol
more information may be found at the Nimblegen website

extract_protocol: Genomic DNA was extracted from the chromatin according to the protocol described in Ekwall & Partridge (1999) Chromosome Structural Analysis: A Practical Approach Vol. 200 p39-57

tag: Chromatin was prepared from 4-14 hour old Canton-S strain embryos and immuno-precipitated with anti-H3K9me2 antibody

tag: Chromatin was prepared from 4-14 hour old Canton-S strain embryos and total genomic DNA was extracted without prior immuno-precipitation


title: MCF10A E2F3 2

description:
Simple annotation: Cell-line, Breast
Image: http://jdemeter-smd-banjo.stanford.edu:8000/MicroArray/gifs/2007-08/76297.gif
Cell Line: E2F3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 11:25:48; Parameter PMT Volts = 550; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 33703; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 11:25:48; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 277448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: MCF10A E2F3 2

tag: MCF10A E2F3 2


title: B37xB73 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B37xB73

value: B37xB73; Stage:11-day old seedling, all aerial tissue


title: Mo17 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Mo17

value: Mo17; Stage:11-day old seedling, all aerial tissue


title: B73 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B73

value: B73; Stage:11-day old seedling, all aerial tissue


title: B37 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B37

value: B37; Stage:11-day old seedling, all aerial tissue


title: B84 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B84

value: B84; Stage:11-day old seedling, all aerial tissue


title: B84xB73 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B84xB73

value: B84xB73; Stage:11-day old seedling, all aerial tissue


title: Patient 2, Pre-Sirolimus

type: mixed

molecule: nuclear RNA

source_name: Glioma biopsy, Patient 2, Pre-Sirolimus

source_name: Normal Female DNA

value: female'


title: Su(var)3-9 H3K9,14Ac/total

data_processing: ChIP/reference signal ratios were calculated from the raw signal intensities and normalized by the median of the entire array.

tag: Chromatin was prepared from 4-14 hour old Su(var)3-9 (allele 06) strain embryos and immuno-precipitated with antibody against histone H3 acetylated at K9 and K14

tag: Chromatin was prepared from 4-14 hour old Su(var)3-9 (allele 06) strain embryos and total genomic DNA was extracted without prior immuno-precipitation


title: MCF10A MYC+CSN5

description:
Simple annotation: Cell-line, Breast
Image: http://jdemeter-smd-banjo.stanford.edu:8000/MicroArray/gifs/2007-08/76295.gif
Cell Line: MYC+CSN5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 400, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 12:20:36; Parameter PMT Volts = 520; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 33756; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 12:20:36; Parameter PMT Volts = 820; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 277501; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: MCF10A MYC+CSN5

tag: MCF10A MYC+CSN5


title: Su(var)3-9 H3K9me2/total

tag: Chromatin was prepared from 4-14 hour old Su(var)3-9 strain (allele 06) embryos and immuno-precipitated with anti-H3K9me2 antibody

tag: Chromatin was prepared from 4-14 hour old Su(var)3-9 strain (allele 06) embryos and total genomic DNA was extracted without prior immuno-precipitation


title: Oh43xMo17 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: Oh43xB73 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: x13 H3K9me2/H3

description:
ChIP and reference DNA samples were amplified using the ligation-mediated PCR method prior to labeling.
Histone H3 C-terminus ChIP sample was used as reference to control for nucleosome density.

tag: Chromatin was prepared from 4-14 hour old x13 translocation strain embryos and immuno-precipitated with anti-H3K9me2 antibody

tag: Chromatin was prepared from 4-14 hour old x13 translocation strain embryos and immuno-precipitated with anti-histone H3 C-terminus antibody


title: Oh43 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: y cn bw sp H3K9me2/H3

source_name: y cn bw sp_H3K9me2_ChIP

tag: Chromatin was prepared from 4-14 hour old y cn bw sp strain embryos and immuno-precipitated with anti-H3K9me2 antibody

source_name: y cn bw sp_H3_reference

tag: Chromatin was prepared from 4-14 hour old y cn bw sp strain embryos and immuno-precipitated with anti-histone H3 C-terminus antibody


title: MCF10A vector

description:
Simple annotation: Cell-line, Breast
Image: http://jdemeter-smd-banjo.stanford.edu:8000/MicroArray/gifs/2007-08/76292.gif
Cell Line: vector only

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 200, 5200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.02; Parameter Scan Time = 11:49:30; Parameter PMT Volts = 520; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 33725; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.02; Parameter Scan Time = 11:49:30; Parameter PMT Volts = 690; Parameter Scan Date = 2007-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 277470; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: universal reference

source_name: MCF10A vector

tag: MCF10A vector


title: ycbs_H3K9me2/total

description: ChIP and reference DNA samples were amplified using the GenomePlex Whole Genome Amplification Kit (Sigma) prior to labeling.

source_name: y cn bw sp_total_reference

tag: Chromatin was prepared from 4-14 hour old y cn bw sp strain embryos and total genomic DNA was extracted without prior immuno-precipitation


title: x13 H3K9me2/total

tag: Chromatin was prepared from 4-14 hour old x13 translocation strain embryos and total genomic DNA was extracted without prior immuno-precipitation


title: B37xB73 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414

tag: Genotype


title: y cn bw sp H3K9me2/total


title: y cn bw sp H3K9,14Ac/total

source_name: y cn bw sp_H3K9,14Ac_ChIP

tag: Chromatin was prepared from 4-14 hour old y cn bw sp strain embryos and immuno-precipitated with antibody against histone H3 acetylated at K9 and K14


title: Oh43xB73 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43xB73


title: B84xB73 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: Mo17 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: Oh43xMo17 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43xMo17


title: Mo17 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: B37 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: B84xB73 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: Oh43 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Oh43


title: B37 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: B73 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: B37xB73 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B37xB73


title: B73 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B73


title: T98G 8 hr LY294002 vs Untreated Cy3-Cy5 rep 1

status: Public on Jan 24 2008

city: Boston

first: Geoffrey

last: Cooper

state: MA

address: 5 Cummington St

institute: Boston University

description: For each treated sample, three independent replicate microarray experiments were performed.

hyb_protocol: For each slide, 4 micrograms of both treated and untreated cyanine-labeled aRNA samples were combined with a hybridization buffer (2.3X SSC, 18 mM HEPES, 0.2 mg/ml BSA, 0.6 mg/ml poly(A), 0.2% SDS), heat denatured for 3 minutes at 95 degrees C, and applied to microarrays under a LifterSlip coverslip (Erie Scientific).  The slides were placed in a hybridization chamber (Dietech) and incubated in a 63 degree C water bath for 16 hr.  Following hybridization, the slides were successively washed in 0.6X SSC with 0.025% SDS, 0.05X SSC, and water, then dried by centrifugation at 1000 rpm for 3 min.

scan_protocol: The microarrays were scanned with an Axon 4000B scanner and adaptive spot segmentation performed with GenePix Pro software (version 5.0) (Axon Instruments).

data_processing: Triplicate dye-swap, background-subtracted median intensity values were used as input to the LIMMA analysis package (Smyth, 2005) in Bioconductor (Gentleman et al., 2004), and average LOESS-corrected log2 ratios were used to estimate differential gene expression after LY294002 treatment. Genes with a change in expression greater than or equal to 1.87 fold (log2 0.9) relative to untreated samples and false discovery rate (FDR)-corrected (Benjamini et al., 1995) moderated t-test p-values less than 0.01 were considered differentially expressed.

molecule: polyA RNA

source_name: Proliferating T98G cells (untreated)

label_protocol: Starting with 100 ng of poly(A)+ RNA, one round of RNA amplification was performed with the MessageAmp aRNA Amplification Kit (Ambion) using a 4:1 amino-allyl UTP:UTP ratio for aRNA incorporation.  For each sample, 8 micrograms of aRNA was coupled to N-hydroxysuccinimidyl esters of cyanine-3 or cyanine-5 (Amersham).  Following clean-up, treated and untreated aRNA samples with opposing cyanine labels were combined, concentrated, and treated with a fragmentation reagent (Ambion) according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent (Invitrogen) followed by poly(A)+ RNA isolation with an Oligotex mRNA Midi Kit (Qiagen) according to each manufacturer's protocol.

treatment_protocol: T98G human glioblastoma cells were grown in Minimal Essential Medium (Invitrogen) containing 10% fetal bovine serum (HyClone) and 100 units/ml of penicillin/streptomycin (Invitrogen). Cells were cultured for 48 hours, at which time they were actively proliferating with a doubling time of approximately 20 hours. If called for, LY294002 (Biomol) was added to a final concentration of 50 uM.

tag: T98G human glioblastoma cells

source_name: Proliferating T98G cells with 8 hr LY294002 treatment


title: B84 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B84


title: T98G 8 hr LY294002 vs Untreated Cy5-Cy3 rep 2


title: T98G 8 hr LY294002 vs Untreated Cy3-Cy5 rep 2


title: T98G 8 hr LY294002 vs Untreated Cy5-Cy3 rep 1


title: Su(var)3-9_H3K9me2/total


title: T98G 4 hr LY294002 vs Untreated Cy3-Cy5 rep 3

source_name: Proliferating T98G cells with 4 hr LY294002 treatment


title: T98G 8 hr LY294002 vs Untreated Cy3-Cy5 rep 3


title: T98G 4 hr LY294002 vs Untreated Cy5-Cy3 rep 3


title: T98G 4 hr LY294002 vs Untreated Cy3-Cy5 rep 2


title: T98G 2 hr LY294002 vs Untreated Cy5-Cy3 rep 3

source_name: Proliferating T98G cells with 2 hr LY294002 treatment


title: T98G 4 hr LY294002 vs Untreated Cy3-Cy5 rep 1


title: T98G 8 hr LY294002 vs Untreated Cy5-Cy3 rep 3


title: T98G 4 hr LY294002 vs Untreated Cy5-Cy3 rep 1


title: T98G 2 hr LY294002 vs Untreated Cy5-Cy3 rep 1


title: T98G 2 hr LY294002 vs Untreated Cy3-Cy5 rep 3


title: DpDf siblings in family segregating for T5-6b DpDf plants; Biological replicate 3

first: Nathan

last: Springer

address: 1445 Gortner Ave

department: Plant Biology

description: No other relevant details

source_name: Zea mays 11-day seedling aerial tissue; DpDf siblings in family segregating for T5-6b DpDf plants

growth_protocol: The T5-6b translocation, backcrossed into B73 maize genetic background for over 10 generations, was available from the University of Minnesota collection.  The interchange T5-6b possesses a break at 5S.1 (ca. 300 cM on IBM2 2004 Neighbors genetic map) and between the middle and distal chromomere of the satellite of 6S (break occurs prior to 50 cM on IBM2 2004 Neighbors genetic map).  Duplicate-Deficient (DpDf) heterozygous plants were identified among progeny derived from crossing a female B73/T5-6b translocation heterozygote by a male B73 plant.  The chromosome constitution of DpDf heterozygous plants is normal for all chromosomes except 5 and 6.  The DpDf plants contain one normal chromosome 6 and one 65 chromosome that is lacking the terminal chromomere of the chromosome 6 satellite and contains ~90% of the short arm of chromosome 5.  Four biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 300C and night temperature of 220C) and sampled for gene expression on the 11th day after planting between 8:00 and 9:00 am.  The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected.  For each biological replicate, sibling seeds produced by self pollination of a DpDf plant that segregate for wild-type and DpDf plants were planted individually and thirty plants were collected and genotyped using an SSR marker (bnlg161) that is tightly linked to the translocation breakpoint on chromosome 5.  A pool of twelve wild-type plants and a separate pool of twelve DpDf plants were generated from each of the biological replicates.  The sampled tissues were flash frozen in liquid nitrogen and stored at -80 0C prior to RNA isolation.

extract_protocol: For seedling RNA isolation, tissues from 12 seedlings/genotype/biological replicate were pooled and ground in liquid nitrogen. RNAs were extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). Resuspended RNAs were purified further using the RNeasy system, according to the manufacturer’s instructions (QIAGEN, Valencia, CA).

value: DpDf siblings (B73 background); Stage:11-day seedling, all aerial tissue; Seed Source:49647-3self


title: T98G 2 hr LY294002 vs Untreated Cy3-Cy5 rep 2


title: Wild-type siblings in family segregating for T5-6b DpDf plants; Biological replicate 3

description: No other relevant details

source_name: Zea mays 11-day seedling aerial tissue; wild-type siblings in family segregating for T5-6b DpDf plants

value: Wild-type siblings (B73 background); Stage:11-day seedling, all aerial tissue; Seed Source:49647-3self


title: T98G 4 hr LY294002 vs Untreated Cy5-Cy3 rep 2


title: Wild-type siblings in family segregating for T5-6b DpDf plants; Biological replicate 4

description: No other relevant details

value: Wild-type siblings (B73 background); Stage:11-day seedling, all aerial tissue; Seed Source:49646-1self


title: T98G 2 hr LY294002 vs Untreated Cy3-Cy5 rep 1


title: DpDf siblings in family segregating for T5-6b DpDf plants; Biological replicate 4

description: No other relevant details

value: DpDf siblings (B73 background); Stage:11-day seedling, all aerial tissue; Seed Source:49646-1self


title: Wild-type siblings in family segregating for T5-6b DpDf plants; Biological replicate 2

description: No other relevant details

growth_protocol: The T5-6b translocation, backcrossed into B73 maize genetic background for over 10 generations, was available from the University of Minnesota collection.  The interchange T5-6b possesses a break at 5S.1 (ca. 300 cM on IBM2 2004 Neighbors genetic map) and between the middle and distal chromomere of the satellite of 6S (break occurs prior to 50 cM on IBM2 2004 Neighbors genetic map) [18, 19].  Duplicate-Deficient (DpDf) heterozygous plants were identified among progeny derived from crossing a female B73/T5-6b translocation heterozygote by a male B73 plant.  The chromosome constitution of DpDf heterozygous plants is normal for all chromosomes except 5 and 6.  The DpDf plants contain one normal chromosome 6 and one 65 chromosome that is lacking the terminal chromomere of the chromosome 6 satellite and contains ~90% of the short arm of chromosome 5.  Four biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 300C and night temperature of 220C) and sampled for gene expression on the 11th day after planting between 8:00 and 9:00 am.  The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected.  For each biological replicate, sibling seeds produced by self pollination of a DpDf plant that segregate for wild-type and DpDf plants were planted individually and thirty plants were collected and genotyped using an SSR marker (bnlg161) that is tightly linked to the translocation breakpoint on chromosome 5.  A pool of twelve wild-type plants and a separate pool of twelve DpDf plants were generated from each of the biological replicates.  The sampled tissues were flash frozen in liquid nitrogen and stored at -80 0C prior to RNA isolation.


title: DpDf siblings in family segregating for T5-6b DpDf plants; Biological replicate 2

description: No other relevant details


title: Wild-type siblings in family segregating for T5-6b DpDf plants; Biological replicate 1

description: No other relevant details

value: Wild-type sibling (B73 background); Stage:11-day seedling, all aerial tissue; Seed Source:49647-3self


title: placenta_G9aKO_rep#1

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: Comparison of gene expression between G9a-/- and wildtype placentae.

hyb_protocol: 15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol. Standard protocol.

scan_protocol: An Affymetrix Scanner 3000 was used to quantify the signal. Standard protocol.

data_processing: MAS5/GCOS: TGT=500, otherwise default values.

organism: Mus musculus

source_name: pooled placentae, 9.5 dpc, G9a-/-

label_protocol: RNA was quantified on an Agilent Bioanalyser and 3µg were used to prepare biotin-labeled cRNA target, as prescribed in the Affymetrix expression manual (Affymetrix, 2004). The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.

extract_protocol: Total RNAs were extracted using Trizol reagent (Invitrogen).

tag: Strain

value: The G9a gene was trapped by insertion of a beta-galactosidase-neomycin phosphotransferase (beta-geo) construct comprising a splice acceptor (Sutherland et al. 2001). We used a G9a-trapped ES cell line, ES62, to generate chimaeric mice by blastocyst injection. Germ line transmission was obtained from these chimaeras. The obtained transgenic line was maintained in a hemizygous state and was crossed for four generations to C57BL/6 mice. Concomitantly, a second line was derived by back-crossing to a (M. spretus) congenic mouse line, SDP711. G9a-/- embryos and placentas were obtained by inter-crossing these two lines.

tag: Age

tag: Tissue

value: placenta.


title: placenta_G9aKO_rep#1_430B


title: U937 cells treated with ultrasound (control-2)

status: Public on Jan 23 2008

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: Human lymphoma U937 cells were cultured at 37°C (non-treatment; control).

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: Human lymphoma U937 cells, untreated (control-2)

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K.K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: Human lymphoma U937 cells


title: Heart 1

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Heart 1

hyb_protocol: Standard Affy

scan_protocol: Standard Affy

data_processing: GCOS

organism: Rattus norvegicus

source_name: Heart (left vent)

label_protocol: Standard Affy

extract_protocol: Standard Affy

tag: Young adult SD rat


title: Heart 5

description: Heart 5


title: DpDf siblings in family segregating for T5-6b DpDf plants; Biological replicate 1

description: No other relevant details


title: Heart 6

description: Heart 6


title: U937 cells treated with ultrasound (treatment-1)

description: U937 cells, a human lymphoma cell line, were treated with low intensity pulsed ultrasound (0.3 W/cm2 for 1 min) and followed by incubation for 3 h at 37°C. Non-treated cells were served as control.

source_name: Human lymphoma U937 cells, treated with ultrasound (treatment-1)


title: Heart 2

description: Heart 2


title: placenta_WT_rep#1

source_name: pooled placentae, 9.5 dpc, wildtype


title: placenta_WT_rep#1_430B


title: Heart 3

description: Heart 3


title: B84 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: IL-22+IL-17, biol rep 3

city: Pittsburgh

first: Shean

last: Aujla

state: PA

address: 3460 Fifth Ave

department: Division of Pulmonary Medicine, Allergy and Immunology

institute: Children's Hospital of Pittsburgh

description: gene expression data - HBEs stim with IL-22+17

hyb_protocol: Following fragmentation, 6.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome 133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 with 7G upgrade

data_processing: RMA (log2-transformed)

source_name: HBE stimulated with IL-22+17

label_protocol: Biotinylated cRNA were prepared using Ambion TotalPrep kit from 395 ng total RNA according to manufacturer's instructions

growth_protocol: Primary HBE cells were grown on semi permeable filters, were polarized and well differentiated and grown at air liquid interface

extract_protocol: Semipermeable membranes were placed in trizol, and trizol extraction of total RNA was performed

treatment_protocol: Cells were stimulated with media, or 20ng/mL human recombinant IL-22, or 10ng/mL hu recombinant IL-17, or both cytokines for 24 hrs

tag: Primary HBEs


title: RNAi_9dpi

organism: Ixodes scapularis

label_protocol: Total RNA (5 µg) were labeled using the 3DNA Array900 kit with Alexa Fluor dyes (Genisphere, Hatfield, PA, USA), Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60mm LifterSlips (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions.

extract_protocol: Total RNA was prepared from subolesin dsRNA- and saline-injected ticks at 6 and 9 dpi (5 and 8 days of feeding) using the RNeasy Mini Kit (Qiagen) including the on-column DNA digestion with the RNase-free DNase set following manufacturer’s instructions.

tag: I. scapularis female ticks 9 days following RNAi treatment

tag: I. scapularis female ticks 9 days following saline treatment


title: media, biol rep 2

description: gene expression data - HBEs stim with media

source_name: HBE stimulated with media


title: IL-17, biol rep 1

description: gene expression data - HBEs stim with IL-17

source_name: HBE stimulated with IL-17


title: IL-17, biol rep 2


title: RNAi_9dpi_ds

description: Normalized (global median) ratio values obtained for each probe were averaged across replicates. Significant differences were defined as those displaying an average expression fold change greater than 2-fold (log (base 2) ratio ≥ 1.0).

tag: I. scapularis female ticks 6 days following saline treatment


title: IL-22, biol rep 3

description: gene expression data - HBEs stim with IL-22

source_name: HBE stimulated with IL-22


title: U937 cells treated with ultrasound (treatment-2)

source_name: Human lymphoma U937 cells, treated with ultrasound (treatment-2)


title: IL-22+IL-17, biol rep 1


title: RNAi_6dpi_ds

tag: I. scapularis female ticks 6 days following RNAi treatment


title: RNAi_6dpi


title: IL-22, biol rep 2


title: IL-22+IL-17, biol rep 2


title: U937 cells treated with ultrasound (control-1)

source_name: Human lymphoma U937 cells, untreated (control-1)


title: media, biol rep 1


title: media, biol rep 3


title: IL-17, biol rep 3


title: Heart 4

description: Heart 4


title: IL-22, biol rep 1


title: 16 min acid stress replicate 3

status: Public on Jan 21 2008

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

description: biological replicate 1 of 2, technical replicate 3 of 3

hyb_protocol: For each microarray experiment, the cDNA probes from one acid shock condition (e.g. 2 min post-acid shock) were individually co-hybridized with cDNA probes from the relevant control sample (cells exposed to MH-MES pH 7.0 for the in vitro experiments or cells grown in vitro in biphasic MH cultures for the in vivo experiment). The fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 µl of water, to which was added 2.5 µl of salmon sperm DNA (10 mg/ml), 9 µl of 20x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7), 0.36 µl of 10% sodium dodecyl sulfate (SDS), and 9 µl of formamide. Prior to hybridization, microarray slides were prehybridized at 42°C for 45 min in prehybridization buffer (25% formamide, 5x SSC buffer, 0.1% SDS, and 1% bovine serum albumin), rinsed with water, and dried by spinning. The probe was denatured by boiling for 2 min, followed by cooling to 42°C. The probe was then applied to the microarray slide under a coverslip, placed in a humidified chamber (ArrayIt), and incubated at 42°C overnight. Following hybridization, slides were washed in 2x SSC-0.1% SDS for 5 min at 42°C, 0.1x SSC-0.1% SDS for 10 min at room temperature, and four times in 0.1x SSC for 1 min at room temperature. Slides were then rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) wavelengths using a laser-activated confocal scanner (ScanArray Gx, Perkin Elmer) at a 10µm resolution.

data_processing: Spot registration was optimized manually, and the fluorescence intensities of each spot were collected using ScanArray Express software (Perkin Elmer). Spots were excluded from analysis if they were present in areas of slide abnormalities or if their fluorescent mean intensities were below three times the standard deviation of the background in both channels. The fluorescence intensity of all remaining spots was normalized using locally weighted linear regression (LOWESS), the ratio of the mean Cy5:Cy3 values was log2 transformed.

organism: Campylobacter jejuni

source_name: total RNA from C. jejuni at pH 7

label_protocol: Total RNA was converted to cDNAs in the presence of aminoallyl-dUTP with Superscript II (Invitrogen) at 42°C. The reverse transcription reaction was performed as follows: 16 µg of total RNA was combined with 10 µg of random hexamers in a 34.35-µl reaction mixture containing 8 µl of 5x Superscript II reverse transcriptase buffer and 2 µl of 0.1 M dithiothreitol. After a 5-min incubation at 65°C, the reaction mixture was brought to a final volume of 40 µl by adding (final concentrations): 0.5 mM each of dGTP, ATP, and CTP; 0.16 mM dTTP; 0.34 mM aminoallyl-dUTP; and 2 µl of Superscript II and incubated at 42°C for 120 min. At the end of the first-strand synthesis, the reaction was stopped and the RNA was hydrolyzed by adding 4 µl of 50 mM EDTA and 2 µl of 10 N NaOH and incubating at 65°C for 20 min. This reaction was neutralized by adding 4 µl of 5 M acetic acid. The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 450 µl of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 8,000 x g. This washing step was repeated three times. After the last wash, the aminoallyl-labeled probes were concentrated to less than 8 µl under vacuum in a SpeedVac and adjusted to a final volume of 10 µl by adding 1 µl of 1 M sodium carbonate (pH 9.0) and water. The resulting aminoallyl-labeled cDNA was coupled to monoreactive fluors (Amersham) by adding 10 µl of dimethyl sulfoxide containing one-sixth of one reaction vial FluoroLink indocarbocyanine or indodicarbocyanine dye and incubating for 45 min at room temperature in the dark. This reaction was quenched by adding 4.5 µl of 4 M hydroxylamine and incubating for 15 min at room temperature in the dark.

growth_protocol: Bacteria were maintained at 37°C on Mueller-Hinton (MH) agar plates under microaerophilic conditions (83% N2, 4% H2, 8% O2 and 5% CO2) in a MACS-VA500 microaerophilic workstation (Don Whitley, West Yorkshire, England). For in vitro pH studies, bacteria were grown to mid-logarithmic phase in biphasic MH medium (equal volume of MH broth layered on top of MH agar in a tissue culture flask) at 37°C in the MACS-VA500 workstation.

extract_protocol: Immediately after collection of samples for RNA extraction, 0.1 volumes of cold RNA degradation stop solution (10% (v/v) buffer-saturated phenol in ethanol) were added to prevent RNA turnover (14). Cells were collected by centrifugation (8, 000 x g, 10 min, 4°C) and the cell pellet was resuspended in TE buffer (50 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.5 mg mL-1 (final concentration) lysozyme. Total RNA was extracted using a hot phenol-chloroform method, precipitated with ethanol, and resuspended in RNase-free H2O. The RNA preparation was treated with DNase I to remove any contaminating genomic DNA, further purified using a QIAGEN RNeasy mini Kit (QIAGEN, Valencia, CA), and quantitated using either the RiboGreen RNA quantitation kit (Molecular Probes, Eugene, OR) or A260 values. RNA integrity was assessed by agarose gel electrophoresis, and PCR amplification was used to confirm that the preparation was free of genomic DNA. RNA samples were stored at -80°C.

treatment_protocol: In order to identify genes whose expression was up- or down-regulated in response to acid shock in vitro, C. jejuni gene expression was monitored over a 20 min period following acid shock. Briefly, bacteria were grown under microaerophilic conditions in biphasic MH medium containing 25 mL of MH broth buffered at pH 7.0 using 100 mM 2-[N-morpholino] ethane sulfonic acid (MES). The pH of the spent culture medium was within 0.1 units of the starting pH. At mid-log phase (O.D.600 = 0.9), 5 mL of the bacterial culture was transferred to a biphasic medium containing 20 mL of MH-MES broth buffered to pH 4.5 (the addition of culture did not alter the pH of the medium). Total RNA was extracted from samples taken 2, 4, 12, 16 and 20 min after the acid challenge. For the control samples, 5 mL of the bacterial culture was transferred to a biphasic medium containing 20 mL of MH-MES broth buffered to pH 7.0, and samples were collected after 2, 4, 12, 16 and 20 min.

tag: mid-log phase

source_name: total RNA from C. jejuni exposed to pH 4.5 for 16 min


title: 16 min acid stress replicate 1

description: biological replicate 1 of 2, technical replicate 1 of 3


title: 16 min acid stress replicate 2

description: biological replicate 1 of 2, technical replicate 2 of 3


title: 12 min acid stress replicate 4

description: biological replicate 2 of 2, technical replicate 1 of 3

source_name: total RNA from C. jejuni exposed to pH 4.5 for 12 min


title: 12 min acid stress replicate 3


title: 12 min acid stress replicate 5

description: biological replicate 2 of 2, technical replicate 2 of 3


title: U937 VCP7 siRNA undiff.

city: Hannover

first: Doris

last: Steinemann

state: Niedersachsen

department: Cell and Molecular Pathology, Theoretische Institute II

country: Germany

institute: Medical School Hannover

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77709.gif
For transfection, the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative control, and Negative Control siRNA AF488 as a FITC-conjugated negative control (all from Qiagen, Hilden, Germany), respectively. After transfection, the cells were immediately transferred into pre-warmed culture medium, supplemented with 10% FCS.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Doris,,Steinemann

source_name: control

growth_protocol: Hofmann_cell_culture; Human U937 myeloid leukemia cells were grown in RPMI 1640 medium containing 10%  fetal calf serum (Biochrom, Hannover, Germany) supplemented with 100 units/ml  penicillin, 100 ug/ml streptomycin and 2 mM L-glutamine (PAA Laboratories  GmbH, Culbe, Germany). The cells were treated with 10 nM TPA (Sigma, St.  Louis, MO, USA) for up to 72 h. The long term culture of adherent  TPA-differentiated U937 cells was performed in the absence of TPA by changing  the culture medium every 3 days until the cells entered the  retrodifferentiation program.; Protocol Type = Biological Sample; Performer: Doris,,Steinemann

extract_protocol: Hofmann_RNA_isolation; About 5x106 cells were lysed in 2 ml TRIZOL Reagent (Invitrogen, Karlsruhe,  Germany) and incubated for 5 min at room temperature. After addition of 400 ul  chloroform, the samples were mixed vigorously and then centrifuged for 15  min/12000 rpm at 4uC. An aliquot of 350 ul of the aqueous upper phase was  incubated for 5 min at 25uC and treated according to the RNeasy Mini Kit  protocol (Qiagen, Hilden, Germany). To determine the RNA concentration and  integrity, the isolated RNA was analyzed in the Agilent 2100 Bioanalyzer  (Agilent Technologies, Bublingen, Germany) using the RNA 6000 Nano LabChip Kit  (Agilent Technologies) according to the manufacturer's protocol.; Protocol Type = Extract preparation; Performer: Doris,,Steinemann

treatment_protocol: Hofmann_siRNA_transfection; Transfection of the cells was performed according to the manufacturer's protocol  (amaxa GmbH, Cologne, Germany). Briefly, 1x106 U937 cells were harvested and  resuspended in 100 ul Nucleofector Solution V (amaxa). The cell suspension was  mixed with 1 ug siRNA, placed in a sterile electroporation cuvette and  subjected to program T20 using the Nucleofector II (amaxa). For transfection,  the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA  Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative  control, and Negative Control siRNA AF488 as a FITC-conjugated negative  control (all from Qiagen, Hilden, Germany), respectively. After transfection,  the cells were immediately transferred into pre-warmed culture medium,  supplemented with 10% FCS. To evaluate the transfection efficiency, U937  controls and cells transfected with Negative Control siRNA AF488 were  harvested after 5 h, washed twice with PBS and subjected to the Galaxy flow  cytometer (Dako) using FloMax analysis software (Partec). For VCP/p97 Western  blot analysis, the transfected cells were harvested 72 h post transfection and  treatment with 10 nM TPA was performed for 24 h.; Protocol Type = Treatment; Performer: Doris,,Steinemann

tag: control

source_name: probe

tag: probe


title: U937 TPA VCP7 siRNA diff.

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77711.gif
For transfection, the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative control, and Negative Control siRNA AF488 as a FITC-conjugated negative control (all from Qiagen, Hilden, Germany), respectively. After transfection, the cells were immediately transferred into pre-warmed culture medium, supplemented with 10% FCS.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 4280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Doris,,Steinemann


title: 20 min acid stress replicate 1

source_name: total RNA from C. jejuni exposed to pH 4.5 for 20 min


title: 20 min acid stress replicate 3


title: 20 min acid stress replicate 5


title: 16 min acid stress replicate 4


title: 16 min acid stress replicate 6

description: biological replicate 2 of 2, technical replicate 3 of 3


title: 20 min acid stress replicate 2


title: 16 min acid stress replicate 5


title: 20 min acid stress replicate 4


title: 20 min acid stress replicate 6


title: T98G 2 hr LY294002 vs Untreated Cy5-Cy3 rep 2

description: For each treated sample, three independent replicate microarray experiments were performed.

source_name: Proliferating T98G cells with 2 hr LY294002 treatment

source_name: Proliferating T98G cells (untreated)


title: U937 VCP6 TPA diff. siRNA

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77710.gif
For transfection, the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative control, and Negative Control siRNA AF488 as a FITC-conjugated negative control (all from Qiagen, Hilden, Germany), respectively. After transfection, the cells were immediately transferred into pre-warmed culture medium, supplemented with 10% FCS.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Doris,,Steinemann


title: 12 min acid stress replicate 2


title: U937 TPA VCP siRNA

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-01/72023.gif
For transfection, the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative control, and Negative Control siRNA AF488 as a FITC-conjugated negative control (all from Qiagen, Hilden, Germany), respectively. After transfection, the cells were immediately transferred into pre-warmed culture medium, supplemented with 10% FCS.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Doris,,Steinemann Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.36; Parameter Scan Time = 10:22:40; Parameter PMT Volts = 580; Parameter Scan Date = 2007-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 68202; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84581]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Doris,,Steinemann Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.36; Parameter Scan Time = 10:22:40; Parameter PMT Volts = 620; Parameter Scan Date = 2007-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 68183; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84581]; Parameter Laser Power = 3.25; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Doris,,Steinemann


title: 12 min acid stress replicate 6


title: U937 VCP6 siRNA undiff.

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77708.gif
For transfection, the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative control, and Negative Control siRNA AF488 as a FITC-conjugated negative control (all from Qiagen, Hilden, Germany), respectively. After transfection, the cells were immediately transferred into pre-warmed culture medium, supplemented with 10% FCS.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 5200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Doris,,Steinemann


title: 4 min acid stress replicate 6

source_name: total RNA from C. jejuni exposed to pH 4.5 for 4 min


title: 4 min acid stress replicate 4


title: 4 min acid stress replicate 5


title: 4 min acid stress replicate 3


title: 2 min acid stress replicate 6

source_name: total RNA from C. jejuni exposed to pH 4.5 for 2 min


title: 4 min acid stress replicate 2


title: 4 min acid stress replicate 1


title: 2 min acid stress replicate 5


title: pH 7 versus pH6.5 replicate 2

hyb_protocol: The labeled cDNA probes from each acid stress condition (e.g. pH 6.5) were individually co-hybridized with labeled-cDNA probes from cells grown at pH 7.0 on microarray slides. The fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 µl of water, to which was added 2.5 µl of salmon sperm DNA (10 mg/ml), 9 µl of 20x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7), 0.36 µl of 10% sodium dodecyl sulfate (SDS), and 9 µl of formamide. Prior to hybridization, microarray slides were prehybridized at 42°C for 45 min in prehybridization buffer (25% formamide, 5x SSC buffer, 0.1% SDS, and 1% bovine serum albumin), rinsed with water, and dried by spinning. The probe was denatured by boiling for 2 min, followed by cooling to 42°C. The probe was then applied to the microarray slide under a coverslip, placed in a humidified chamber (ArrayIt), and incubated at 42°C overnight. Following hybridization, slides were washed in 2x SSC-0.1% SDS for 5 min at 42°C, 0.1x SSC-0.1% SDS for 10 min at room temperature, and four times in 0.1x SSC for 1 min at room temperature. Slides were then rinsed with distilled water and dried by centrifugation.

source_name: total RNA from C. jejuni grown at pH 7

label_protocol: Total RNA from each growth condition was converted to cDNAs in the presence of aminoallyl-dUTP with Superscript II (Invitrogen) at 42°C. The reverse transcription reaction was performed as follows: 16 µg of total RNA was combined with 10 µg of random hexamers in a 34.35-µl reaction mixture containing 8 µl of 5x Superscript II reverse transcriptase buffer and 2 µl of 0.1 M dithiothreitol. After a 5-min incubation at 65°C, the reaction mixture was brought to a final volume of 40 µl by adding (final concentrations): 0.5 mM each of dGTP, ATP, and CTP; 0.16 mM dTTP; 0.34 mM aminoallyl-dUTP; and 2 µl of Superscript II and incubated at 42°C for 120 min. At the end of the first-strand synthesis, the reaction was stopped and the RNA was hydrolyzed by adding 4 µl of 50 mM EDTA and 2 µl of 10 N NaOH and incubating at 65°C for 20 min. This reaction was neutralized by adding 4 µl of 5 M acetic acid. The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 450 µl of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 8,000 x g. This washing step was repeated three times. After the last wash, the aminoallyl-labeled probes were concentrated to less than 8 µl under vacuum in a SpeedVac and adjusted to a final volume of 10 µl by adding 1 µl of 1 M sodium carbonate (pH 9.0) and water. The resulting aminoallyl-labeled cDNA was coupled to monoreactive fluors (Amersham) by adding 10 µl of dimethyl sulfoxide containing one-sixth of one reaction vial FluoroLink indocarbocyanine or indodicarbocyanine dye and incubating for 45 min at room temperature in the dark. This reaction was quenched by adding 4.5 µl of 4 M hydroxylamine and incubating for 15 min at room temperature in the dark.

growth_protocol: To study the effect of pH on C. jejuni growth and on its transcriptional profile, bacteria were grown to stationary phase in biphasic MH medium under microaerophilic conditions (83% N2, 4% H2, 8% O2 and 5% CO2) , and an aliquot of the culture equivalent to O.D.600 = 0.05 was used to inoculate biphasic MH-MES (2-[N-morpholino] ethane sulfonic acid) medium at pH 7.0, 6.5, 6.0 and 5.5. This medium was prepared by layering MES-buffered MH broth (pH 7.0, 6.5, 6.0 or 5.5) over a layer of solid MH-MES agar at the same pH. MES was used at a concentration of 100 mM, and medium pH was adjusted with NaOH. Bacterial growth was monitored spectrophotometrically at 600 nm by removing 100 µL samples at various time points over 40 h.

extract_protocol: RNA was extracted from cells grown to early mid-logarithmic phase (O.D.600 = 0.9) at 37ºC under microaerophilic conditions. Briefly, RNA turnover was prevented by mixing each sample (25 mL) with a cold RNA stabilization solution (2.5 mL of 10% (v/v) buffer-saturated phenol in ethanol) on ice. Next, the cells were collected by centrifugation (10 min, 6,000 x g, 4°C), cell pellets were resuspended in TE buffer (50 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.5 mg mL-1 (final concentration) lysozyme, and total RNA was extracted using a hot phenol-chloroform method. RNA was precipitated, resuspended in RNase-free water, and treated with DNase I (Epicentre Biotechnologies, Madison, WI) to remove contaminating DNA. Each RNA sample was further purified using a QIAGEN RNeasy mini kit (QIAGEN, Valencia, CA) and RNA concentration was determined using the RiboGreen RNA quantification reagents (Molecular Probes, Eugene, OR). The samples were screened for contaminating DNA by PCR amplification, and for degradation by agarose gel electrophoresis, prior to conversion into cDNA.

treatment_protocol: To study the effect of pH on gene expression, C. jejuni was grown to mid-log phase at pH 7.0, 6.5, 6.0 and 5.5 in biphasic MH-MES medium and the resulting transcriptional profiles were analyzed by microarray technologies.

source_name: total RNA from C. jejuni grown at pH 6.5


title: pH 7 versus pH6.5 replicate 5


title: pH 7 versus pH6 replicate 6

source_name: total RNA from C. jejuni grown at pH 6


title: 2 min acid stress replicate 2


title: 2 min acid stress replicate 1


title: 2 min acid stress replicate 4


title: pH 7 versus pH6.5 replicate 1


title: pH 7 versus pH6.5 replicate 6


title: pH 7 versus pH6 replicate 4


title: pH 7 versus pH6 replicate 5


title: 12 min acid stress replicate 1


title: U937 VCP siRNA

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-01/72022.gif
For transfection, the following siRNAs were used: GW VAL siRNA Hs_VCP_6 and GW VAL siRNA Hs_VCP_7 to target VCP/p97, AllStars Negative Control siRNA as a negative control, and Negative Control siRNA AF488 as a FITC-conjugated negative control (all from Qiagen, Hilden, Germany), respectively. After transfection, the cells were immediately transferred into pre-warmed culture medium, supplemented with 10% FCS.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Doris,,Steinemann Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.82; Parameter Scan Time = 10:09:13; Parameter PMT Volts = 580; Parameter Scan Date = 2007-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 68181; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84581]; Parameter Laser Power = 3.55; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Doris,,Steinemann Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.82; Parameter Scan Time = 10:09:13; Parameter PMT Volts = 600; Parameter Scan Date = 2007-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 68162; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84581]; Parameter Laser Power = 3.23; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Doris,,Steinemann


title: pH 7 versus pH6 replicate 3


title: pH 7 versus pH6 replicate 1


title: pH 7 versus pH6 replicate 2


title: pH 7 versus pH6.5 replicate 4