title: invivo-replicate6

description: technical replicate 6 of 6

hyb_protocol: The in vivo labeled cDNA was subjected to microarray analysis by competitive hybridization with cDNA derived from C. jejuni grown to mid-log phase in vitro in MH medium (pH 7.0). The two labeled cDNA were pooled and 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 to mid-log phase in vitro in MH medium (pH 7.0)

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 vivo 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: 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: This experiment was performed with colostrum-deprived piglets. Piglets were fed a milk replacer (Multi-purpose milk replacer, Grade A Ultra24, Sav-A-Caf Products) upon arrival four times daily (between 60 to 120 mL per piglet per feeding). C. jejuni NCTC 11168 was grown in biphasic MH cultures under microaerophilic conditions. Cells were collected at mid-log phase (O.D.600 = 0.9) by centrifugation and gently resuspended in MH broth. Prior to inoculation, the piglets were starved for 8 hours.  Two 3-day-old piglets were orally inoculated with 10 mL of a bacterial suspension containing approximately 10e13 viable bacteria.  After 15 min, the piglets were euthanized, and the intact stomachs were excised from the abdominal cavity by ligating the lower end of the oesophagus (next to the cardiac orifice) and the upper end of the duodenum (next to the pyloric orifice). Approximately 5 min following the euthanasia, the stomachs were linearly opened and the stomach contents (~20 mL per stomach) were recovered in 20 mL of a cold RNA degradation stop solution (consisting of 4 mL of 10% buffer saturated phenol in ethanol and 16 mL of PBS buffer). Large particles and epithelial cells were removed from the stomach suspensions by low-speed centrifugation (1,000 x g, 15 min, 4°C).  Thereafter, Campylobacter cells were collected by centrifugation (8, 000  g, 10 min, 4°C).

source_name: total RNA from C. jejuni exposed to the pig stomach for 20 min

tag: stomach transit


title: 2 min acid stress replicate 3

status: Public on Jan 21 2008

type: RNA

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.

molecule: total RNA

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 2 min


title: invivo-replicate4

description: technical replicate 4 of 6


title: invivo-replicate5

description: technical replicate 5 of 6


title: pH 7 versus pH6.5 replicate 3

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: pH7 versus pH5.5 replicate 4

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

source_name: total RNA from C. jejuni grown at pH 5.5


title: invivo-replicate3

description: technical replicate 3 of 6


title: invivo-replicate2

description: technical replicate 2 of 6


title: pH7 versus pH5.5 replicate 3


title: invivo-replicate1

description: technical replicate 1 of 6


title: pH7 versus pH5.5 replicate 1

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


title: pH7 versus pH5.5 replicate 6

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


title: UV-SeV 3663

status: Public on Jan 19 2008

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

country: USA

institute: Washington University School of Medicine

description: epithelial cell response to sendai virus infection

hyb_protocol: Samples were hybridized in duplicate to gene chip U74Av2 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Chips were scanned, and hybridization data were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software.

data_processing: Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004, ver 2.0), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).

label: biotin

organism: Mus musculus

source_name: UV-inactivated Sendai virus infected mouse tracheal epithelial cells.

label_protocol: Poly(A)+ RNA was amplified using RiboAmp (Arcturus, Mountain View, CA), and then labelled with biotin using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY)

growth_protocol: Primary-culture mouse tracheal epithelial cells (mTECs) were established on Transwell membranes using air-liquid interface (ALI) conditions as described previously (Tyner et al, 2006).

extract_protocol: Total RNA was isolated from mTEC cultures using the Micro RNA Isolation kit (Stratagene) and converted to Poly(A)+ RNA.

treatment_protocol: Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Cultures were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) in the apical compartment for 1 h at 37 °C, then removed by washing.  RNA was collected 24 hours after inoculation.

tag: Strain

tag: Gender

value: Male

tag: Tissue

value: primary culture tracheal epithelial cells


title: SeV 3660

source_name: Sendai virus infected mouse tracheal epithelial cells.


title: UV-SeV 3661


title: UV-SeV 3478


title: UV-SeV 3659


title: SeV 3483


title: UV-SeV 3480


title: UV-SeV 3482


title: SeV 3658


title: SeV 3479


title: Ferm. aerob_R1vsR2_ low

status: Public on Jan 18 2008

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

description: Comparing sample R1 vs R2, low PMT setting

hyb_protocol: Agilent hybridization  protocol for Two-color  microarray-based Gene  expression analysis.  Version 5.5

scan_protocol: Using the Scan Array  Express microarray  scanner. 1.Turn on the  scanner and the computer  (in this order) 2.Login:  scanner 3.Double click the  'ScanArray Express' icon  4.Switch on lasers 1 and 3  at least 15 minutes prior to  scanning arrays 5.Click the  'File' button This is to  prevent you from  accidentally turning off the  laser after the 15 minutes  warming-up phase 6.Insert  the slide with the array-side  up and the label towards  the outside. On Agilent  slides the array side is the  side with the label that has  the word "Agilent" on it  7.Press 'Scan | Prescan'  8.Put resolution at 50 m,  select both labels used,  and set PMT values for  both channels 9.Press  'Start' 10.Press 'Palette,'  'Green' as soon as  projection of the image has  started (first dye), select  the red colour as soon as  scanning of the second  layer (second dye) has  started 11.Adjust PMT  values to balance signals  obtained for both  channels. If necessary do  a few low-resolution scans  to obtain a optimal balance  12.Click the 'Scan' button  again 13.Select frame for  high resolution scan, adjust  resolution (to 10 m) and  scan the array for both  dyes 14.Press 'File | Save'  to save the files, 'Save all'  saves both dye layers  "Create a new folder for  each array "'Save all'  saves the signals from both  layers in individual files  15.Switch off the lasers

data_processing: 1.-Used script to split  8-array imagene file of cy3  intensity into eight separate  cy3 files. 2.-Used script to  split 8-array imagene file of  cy5 intensity into eight  separate cy5 files. 3.-For  each indidivual array, a  merge file was produced  consisting of merging the  cy3 and cy5 intensity files  created in step 1 and 2.  The merged file is provided  as supplementary file for  each array. 4.-Background  correction (Mean values)

organism: Lactiplantibacillus plantarum WCFS1

source_name: Sample R2, after growth stagnation

label_protocol: Annealing Mix x µl RNA  preparation (=5µg) y µl  nuclease-free water 1 µl  Random Nonamers 11  µl TOTAL 1. mix  Annealing Mix in a 200  µl PCR tube gently by  pipetting up and down  2. incubate for 5’ 70°C  3. cool at room  temperature for 10’  (annealing) 4. spin down  the mixture to the  bottom of the tube 5.  place on ice Reverse  transcription Reverse  Transcription Mix 4 µl 5x  buffer 2 µl 0.1 M DTT 1  µl dNTP-mix 1 µl  AA-dUTP 1 µl TMIII  (keep only briefly  outside 20°C) 20 µl  TOTAL 1. Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.  Incubate for 3 hrs at  42°C (in PCR-machine)  3. Cool on ice for  immediate purification or  place at 20°C for  storage Degradation of  mRNA 1. Add 2 µl 2,5 M  NaOH 2. Mix (vortex)  and spin down 3.  Incubate for 15 min. at  37°C 4. Add 10 µl 2 M  HEPES free acid 5. Mix  (vortex) and spin down  6. Ready for purification  or store at 20°C  Labelling and  purification of cDNA  with cyanine dyes  Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA" code  RPN5661 Labelling of  amino allyl-modified  cDNA with CyDye 1.  Add the amino allyl  modified cDNA (in 0.1 M  sodium bicarbonate)  directly into one aliquot  of CyDye NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.  Incubate at room  temperature, in the dark  for 60 to 90 minutes 3.  Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4. Mix  by stirring and incubate  at room temperature, in  the dark, for 15 minutes  5. Proceed directly to  purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed  Ge Healthcare kit  "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA" code  RPN5661

extract_protocol: Collecting cells  Quenching Buffer 66.7  mM HEPES (pH 6.5)  60%Methanol Extraction  Mixture (Prepared in a  screw-cap tube) -500 µll  phenol/Chloroform -30  µl10% SDS -30 µl3 M  NaAc (pH 5.2) -500 mg  glass-beads (75-150 µm)  -400 µlTE buffer 1.For  each sample prepare a  tube with Extraction  Mixture 2.Harvest cells  and quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of cell culture  3.Mix and store the  sample at -40°C  4.Centrifuge cells at -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet with  a pre-cooled spatula to  a screw-crap tube with  Extraction Mixture 6.Mix  the cell pellet thoroughly  with Extraction Mixture  by shaking by hand  7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in  the Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary)  9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer  500 µl of the  supernatant to a new  tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with  the "High Pure RNA  Isolation Kit" from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA  in at least 2 aliquots,  one of 20 µl (for  concentration and  quality analysis and  labelling) and one  back-up of 30 µl at  -80°C.

tag: mid exponential growth phase;optical density (600 nm)=1.166

source_name: Sample R1, before growth stagnation

tag: early exponential growth phase;optical density (600 nm)=0.434


title: Ferm. aerob_L1vsL2_low

description: Comparing sample L1 vs L2, low PMT setting

source_name: Sample L2, after growth stagnation

tag: mid exponential growth phase;optical density (600 nm)=0.964

source_name: Sample L1, before growth stagnation

tag: early exponential growth phase;optical density (600 nm)=0.400


title: Ferm. aerob_R1vsR2_high

description: Comparing sample R1 vs R2, high PMT setting


title: pH7 versus pH5.5 replicate 5

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


title: Peripheral blood_male_Vata_techrep2_Ex.set2&3

status: Public on Jan 16 2008

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

country: India

institute: CSIR-Institute Of Genomics and Integrative Biology

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second technical replicate of the Vata male samples

hyb_protocol: The two cRNA samples of each prakriti, one labeled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides. Inter prakriti cohybridization was carried out at 37ºC for 16 hrs.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Analysis was carried out taking two experiments at a time, separately for male and female data. Background subtracted mean values were used for the analysis. All the negative values were removed and only those genes having positive values for all the samples were considered for further analysis.  Values were log2 transformed and lowess normalization. Across array normalization was carried out using quantile normalization method. One-way analysis of variance was adopted to identify differentially expressed genes in all three categories. F-test was carried out in order to reject the hypothesis of equality of three group means. in order to investigate further the nature of differentially expressed genes; we have drawn strip charts and carried out pair wise comparisons using t-test. p-values obtained from ANOVA have been adjusted for multiplicity using Bonferroni method for controlling family wise error rate. Genes at p0.1 level of significance were considered to be significantly different in expression between all three groups.

organism: Homo sapiens

source_name: Peripheral blood cells from vata prakriti males

label_protocol: Three samples of each prakriti were pooled. Experiments for male and female were carried out separately. Double stranded cDNA was synthesized from 15 µg (5 µg each sample) of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. Each pool of Vata, Pitta and Kapha purified cDNA was divided into two halves, one half labeled with Cy5 and other with Cy3  (Amersham Biosciences) using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

extract_protocol: Using EZ-RNA isolation kit (Biological Industries) as per manufacturers protocol.

tag: total RNA from peripheral blood cells of second set of vata prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Ferm. aerob_L1vsL2_high

description: Comparing sample L1 vs L2, high PMT setting


title: pH7 versus pH5.5 replicate 2

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


title: Peripheral blood_male_Vata_rep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third biological replicate of Vata males

tag: total RNA from peripheral blood cells of third set of vata prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_male_Vata_techrep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third technical replicate of the Vata male samples

tag: total RNA from peripheral blood cells of third set of vata prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_male_Vata_rep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second biological replicate of Vata males

tag: total RNA from peripheral blood cells of second set of vata prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_male_Kapha_techrep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third technical replicate of the Kaph male samples

source_name: Peripheral blood cells from Kapha prakriti males

tag: total RNA from peripheral blood cells of third set of Kapha prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_male_Pitta_rep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third biological replicate of Pitta males

source_name: Peripheral blood cells from pitta prakriti males

tag: total RNA from peripheral blood cells of third set of pitta prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_male_Kapha_rep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third biological replicate of Kapha males .

tag: total RNA from peripheral blood cells of third set of Kapha prakriti males of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 2.


title: Peripheral blood_male_Pitta_techrep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third technical replicate of the Pitta male samples

tag: total RNA from peripheral blood cells of third set of pitta prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: PHLMEB genomic DNA 2

type: genomic

city: South San Francisco

first: Adam

middle: S

last: Adler

state: CA

address: 1 DNA Way

institute: Genentech

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66605.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 420, 4200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 30.81; Parameter Scan Time = 10:41:03; Parameter PMT Volts = 650; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 66549; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 30.81; Parameter Scan Time = 10:41:03; Parameter PMT Volts = 710; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 236780; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

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)

molecule: genomic DNA

source_name: male genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: male genomic DNA

source_name: immortal human breast cell line

tag: immortal human breast cell line


title: Peripheral blood_male_Pitta_techrep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second technical replicate of the Pitta male samples

tag: total RNA from peripheral blood cells of second set of pitta prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_male_Pitta_rep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third biological replicate of Pitta males

tag: total RNA from peripheral blood cells of third set of pitta prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1


title: PHLMER genomic DNA 1

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65346.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.52; Parameter Scan Time = 12:27:10; Parameter PMT Volts = 490; Parameter Scan Date = 2005-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 61962; Parameter Focus Position = 5; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.52; Parameter Scan Time = 12:27:10; Parameter PMT Volts = 540; Parameter Scan Date = 2005-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 232259; Parameter Focus Position = 5; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

source_name: PHMLER; transformed human breast cancer cell line

tag: transformed human breast cancer cell line (Elenbaas et al., Genes Dev, 2001)


title: Peripheral blood_male_Pitta_rep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2and 3 experimental sets, for the second biological replicate of Pitta males

tag: total RNA from peripheral blood cells of second set of pitta prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_male_Vata_techrep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first technical replicate of the Vata male samples

tag: total RNA from peripheral blood cells of first set of vata prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_male_Kapha_rep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second biological replicate of Kapha males .

tag: total RNA from peripheral blood cells of second set of Kapha prakriti males of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_male_Vata_rep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third biological replicate of Vata males

tag: total RNA from peripheral blood cells of third set of vata prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1


title: Peripheral blood_male_Kapha_rep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third biological replicate of Kapha males .

tag: total RNA from peripheral blood cells of third set of Kapha prakriti males of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_male_Kapha_techrep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second technical replicate of the Kaph male samples

tag: total RNA from peripheral blood cells of second set of Kapha prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3.


title: PHLMER genomic DNA 3

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65348.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 29.23; Parameter Scan Time = 13:05:45; Parameter PMT Volts = 500; Parameter Scan Date = 2005-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 62001; Parameter Focus Position = 5; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 29.23; Parameter Scan Time = 13:05:45; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 232299; Parameter Focus Position = 5; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Peripheral blood_male_Vata_rep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first biological replicate of Vata males

tag: total RNA from peripheral blood cells of first set of vata prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3


title: Peripheral blood_male_Pitta_techrep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first technical replicate of the Pitta male samples

tag: total RNA from peripheral blood cells of first set of pitta prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: PHMLER_siCSN5_2

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64621.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 5080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 29.38; Parameter Scan Time = 10:27:34; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 59003; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 29.38; Parameter Scan Time = 10:27:34; Parameter PMT Volts = 510; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229371; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

source_name: Universal Reference

tag: Universal Reference

source_name: RNA from PHMLER cells transfected with siCSN5 for 48 hours

treatment_protocol: siRNAs against the  indicated genes were transfected 48 hours before harvesting RNA


title: Peripheral blood_male_Pitta_techrep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third technical replicate of the Pitta male samples

tag: total RNA from peripheral blood cells of third set of pitta prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: PHLMER genomic DNA 2

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65347.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.86; Parameter Scan Time = 12:47:33; Parameter PMT Volts = 490; Parameter Scan Date = 2005-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 61983; Parameter Focus Position = 5; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.86; Parameter Scan Time = 12:47:33; Parameter PMT Volts = 550; Parameter Scan Date = 2005-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 232281; Parameter Focus Position = 5; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: PHMLER_siMYC+CSN5_1

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64622.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 5080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 29.56; Parameter Scan Time = 10:41:25; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 59016; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 29.56; Parameter Scan Time = 10:41:25; Parameter PMT Volts = 520; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229384; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

source_name: RNA from PHMLER cells transfected with siMYC and siCSN5 for 48 hours


title: Peripheral blood_male_Pitta_rep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first biological replicate of Pitta males

tag: total RNA from peripheral blood cells of first set of pitta prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3


title: PHMLER_siGFP_2

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64617.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.34; Parameter Scan Time = 09:30:17; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 58946; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.34; Parameter Scan Time = 09:30:17; Parameter PMT Volts = 520; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229314; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.39; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

source_name: RNA from PHMLER cells transfected with siGFP for 48 hours


title: PHMLER_siCSN5_1

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64620.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 5080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 29.13; Parameter Scan Time = 10:13:37; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 58989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 29.13; Parameter Scan Time = 10:13:37; Parameter PMT Volts = 510; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229356; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: PHLMEB genomic DNA 1

description:
Simple annotation: aCGH, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66604.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 4240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 31.27; Parameter Scan Time = 10:59:52; Parameter PMT Volts = 630; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 66568; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 31.27; Parameter Scan Time = 10:59:52; Parameter PMT Volts = 720; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 236799; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Peripheral blood_male_Kapha_techrep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first technical replicate of the Kaph male samples

tag: total RNA from peripheral blood cells of first set of Kapha prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: PHMLER_siGFP_1

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64616.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.16; Parameter Scan Time = 09:06:35; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 58922; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.16; Parameter Scan Time = 09:06:35; Parameter PMT Volts = 530; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229289; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.39; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: PHMLER_siMYC_1

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64618.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.59; Parameter Scan Time = 09:44:03; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 58960; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.59; Parameter Scan Time = 09:44:03; Parameter PMT Volts = 520; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229327; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

source_name: RNA from PHMLER cells transfected with siMYC for 48 hours


title: PHMLER_siMYC+CSN5_2

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64623.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler 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 = 29.71; Parameter Scan Time = 10:54:41; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 59030; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler 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 = 29.71; Parameter Scan Time = 10:54:41; Parameter PMT Volts = 520; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229397; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.42; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Peripheral blood_male_Kapha_rep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first biological replicate of Kapha males .

tag: total RNA from peripheral blood cells of first set of Kapha prakriti males of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 3.


title: PHMLER_siMYC_2

description:
Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64619.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.86; Parameter Scan Time = 09:58:15; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 58974; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.86; Parameter Scan Time = 09:58:15; Parameter PMT Volts = 520; Parameter Scan Date = 2005-10-18; Parameter Pixel Size = 10; Parameter Laser on time = 229342; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Peripheral blood_male_Kapha_techrep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second technical replicate of the Kaph male samples

tag: total RNA from peripheral blood cells of second set of Kapha prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1.


title: Peripheral blood_male_Vata_techrep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second technical replicate of the Vata male samples

tag: total RNA from peripheral blood cells of second set of vata prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_male_Pitta_techrep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first technical replicate of the Pitta male samples

tag: total RNA from peripheral blood cells of first set of pitta prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_male_Kapha_rep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first biological replicate of Kapha males .

tag: total RNA from peripheral blood cells of first set of Kapha prakriti males of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 2.


title: Peripheral blood_female_Vata_rep2_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4  experimental sets, for the second biological replicate of Vata females

source_name: Peripheral blood cells from vata prakriti females

tag: total RNA from peripheral blood cells of second set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 4


title: Peripheral blood_male_Pitta_rep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second biological replicate of Pitta males

tag: total RNA from peripheral blood cells of second set of pitta prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_female_Pitta_techrep2_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the second technical replicate of the Pitta female samples

source_name: Peripheral blood cells from pitta prakriti females

tag: total RNA from peripheral blood cells of second set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_male_Kapha_techrep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first technical replicate of the Kaph male samples

tag: total RNA from peripheral blood cells of first set of Kapha prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_male_Pitta_rep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first biological replicate of Pitta males

tag: total RNA from peripheral blood cells of first set of pitta prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_male_Pitta_techrep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second technical replicate of the Pitta male samples

tag: total RNA from peripheral blood cells of second set of pitta prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_male_Vata_rep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second biological replicate of Vata males

tag: total RNA from peripheral blood cells of second set of vata prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_male_Kapha_rep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second biological replicate of Kapha males .

tag: total RNA from peripheral blood cells of second set of Kapha prakriti males of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_female_Vata_techrep2_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the second technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of second set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_male_Vata_techrep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first technical replicate of the Vata male samples

tag: total RNA from peripheral blood cells of first set of vata prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Pitta_rep2_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2and 4 experimental sets, for the second biological replicate of Pitta females

tag: total RNA from peripheral blood cells of second set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 4


title: Peripheral blood_female_Kapha_techrep2_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the second technical replicate of the Kaph female samples

source_name: Peripheral blood cells from Kapha prakriti females

tag: total RNA from peripheral blood cells of second set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_male_Vata_techrep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third technical replicate of the Vata male samples

tag: total RNA from peripheral blood cells of third set of vata prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Kapha_rep2_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the second biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of second set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 4.


title: Peripheral blood_female_Vata_rep3_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the third biological replicate of Vata females

tag: total RNA from peripheral blood cells of third set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 4


title: Peripheral blood_female_Kapha_techrep3_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the third technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of third set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_female_Pitta_techrep3_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the third technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of third set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_female_Pitta_rep3_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the third biological replicate of Pitta females

tag: total RNA from peripheral blood cells of third set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 4


title: Peripheral blood_female_Vata_techrep3_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the third technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of third set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_female_Vata_rep1_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the first biological replicate of Vata females

tag: total RNA from peripheral blood cells of first set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 4


title: Peripheral blood_female_Pitta_techrep1_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the first technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of first set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_female_Vata_techrep4_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the fourth technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of fourth set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Vata_techrep4_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the fourth technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of fourth set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_techrep4_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the fourth technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of fourth set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Kapha_rep4_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the fourth biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of fourth set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_female_Kapha_rep4_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the fourth biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of fourth set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 2.


title: Peripheral blood_female_Kapha_techrep4_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the fourth technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of fourth set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Pitta_rep4_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the fourth biological replicate of Pitta females

tag: total RNA from peripheral blood cells of fourth set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3


title: Peripheral blood_female_Kapha_rep1_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the first biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of first set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 4.


title: Peripheral blood_female_Pitta_techrep4_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the fourth technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of fourth set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_male_Kapha_techrep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third technical replicate of the Kaph male samples

tag: total RNA from peripheral blood cells of third set of Kapha prakriti males of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Vata_rep4_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the fourth biological replicate of Vata females

tag: total RNA from peripheral blood cells of fourth set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3


title: Peripheral blood_female_Kapha_techrep4_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the fourth technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of fourth set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Pitta_techrep4_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the fourth technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of fourth set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Kapha_techrep1_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the first technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of first set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_female_Pitta_rep1_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the first biological replicate of Pitta females

tag: total RNA from peripheral blood cells of first set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 4


title: Peripheral blood_female_Vata_rep4_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the fourth biological replicate of Vata females

tag: total RNA from peripheral blood cells of fourth set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_techrep1_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the first technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of first set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 4


title: Peripheral blood_female_Pitta_rep4_Ex.set2&4

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 4 experimental sets, for the fourth biological replicate of Pitta females

tag: total RNA from peripheral blood cells of fourth set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_female_Kapha_techrep4_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the fourth technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of fourth set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Pitta_techrep4_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the fourth technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of fourth set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Pitta_rep4_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the fourth biological replicate of Pitta females

tag: total RNA from peripheral blood cells of fourth set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1


title: Peripheral blood_female_Vata_rep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third biological replicate of Vata females

tag: total RNA from peripheral blood cells of third set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_techrep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of third set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Kapha_techrep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of third set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_techrep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of second set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Pitta_techrep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of third set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_rep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third biological replicate of Vata females

tag: total RNA from peripheral blood cells of third set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1


title: Peripheral blood_female_Pitta_rep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2and 3 experimental sets, for the second biological replicate of Pitta females

tag: total RNA from peripheral blood cells of second set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_female_Pitta_rep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third biological replicate of Pitta females

tag: total RNA from peripheral blood cells of third set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_female_Kapha_techrep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of third set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Kapha_rep3_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the third biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of third set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 2.


title: Peripheral blood_female_Pitta_rep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third biological replicate of Pitta females

tag: total RNA from peripheral blood cells of third set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1


title: Peripheral blood_female_Pitta_techrep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of third set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Kapha_rep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of second set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_female_Vata_techrep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of third set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Kapha_rep3_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the third biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of third set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_female_Kapha_techrep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of second set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3.


title: Fra2-siRNA-low-1

city: Osaka

first: Tokuzo

last: Arao

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Genome Biology

country: Japan

institute: Kinki University School of Medicine

description: Affy

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: a log base 2 transformation was applied to the microarray raw data, and global normalization was used to median over entire array. Genes were excluded if percent of data missing or filtered out exceeds 20%.

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol


title: Peripheral blood_female_Vata_techrep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of first set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Vata_rep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first biological replicate of Vata females

tag: total RNA from peripheral blood cells of first set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3


title: Peripheral blood_female_Pitta_techrep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of second set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Vata_rep2_Ex.set2&3

description: Log2 normalized values of the analyzable spots commonly obtained between 2 and 3 experimental sets, for the second biological replicate of Vata females

tag: total RNA from peripheral blood cells of second set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3.


title: Peripheral blood_female_Kapha_rep3_Ex.set3&4

description: Log2 normalized values of the analyzable spots commonly obtained between 3 and 4 experimental sets, for the third biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of third set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 4.


title: Fra2-siRNA-High-1

description: Affy


title: Peripheral blood_male_Vata_rep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first biological replicate of Vata males

tag: total RNA from peripheral blood cells of first set of vata prakriti males of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Fra2-siRNA-High-2

description: Affy


title: control-siRNA-low-2

description: Affy


title: Peripheral blood_female_Vata_rep4_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the fourth biological replicate of Vata females

tag: total RNA from peripheral blood cells of fourth set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1


title: Peripheral blood_female_Pitta_techrep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of second set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Kapha_rep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of second set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_female_Pitta_rep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second biological replicate of Pitta females

tag: total RNA from peripheral blood cells of second set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_female_Pitta_techrep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first technical replicate of the Pitta female samples

tag: total RNA from peripheral blood cells of first set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_rep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first biological replicate of Vata females

tag: total RNA from peripheral blood cells of first set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: Peripheral blood_female_Vata_techrep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of first set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Kapha_techrep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of second set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1.


title: Fra2-siRNA-low-2

description: affy

hyb_protocol: affymetrix protocol

scan_protocol: affymetrix protocol

label: affy

label_protocol: affymetrix protocol

extract_protocol: affymetrix protocol


title: Peripheral blood_female_Kapha_rep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of first set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 2.


title: Peripheral blood_female_Vata_rep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second biological replicate of Vata females

tag: total RNA from peripheral blood cells of second set of vata prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 1.


title: Peripheral blood_female_Kapha_techrep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of first set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Peripheral blood_female_Vata_techrep2_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the second technical replicate of the Vata female samples

tag: total RNA from peripheral blood cells of second set of vata prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 1


title: Peripheral blood_female_Pitta_rep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first biological replicate of Pitta females

tag: total RNA from peripheral blood cells of first set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 2


title: control-siRNA-High-2

description: Affy


title: Peripheral blood_female_Kapha_rep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of first set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 3.


title: control-siRNA-low-1

description: Affy


title: Peripheral blood_female_Kapha_techrep1_Ex.set1&2

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 2 experimental sets, for the first technical replicate of the Kaph female samples

tag: total RNA from peripheral blood cells of first set of Kapha prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 2


title: Peripheral blood_female_Kapha_rep4_Ex.set1&4

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 4 experimental sets, for the fourth biological replicate of Kapha females .

tag: total RNA from peripheral blood cells of fourth set of Kapha prakriti females of age group 18-40yrs, labeled with Cy3, and compared with values obtained in set 1.


title: control-siRNA-High-1

description: Affy


title: Ler 1

status: Public on Jan 15 2008

first: Ivan

last: Baxter

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

description: DNA sample for Bulk Segregant analysis from http://naturalsystems.uchicago.edu/naturalvariation/methods/ColLerCEL.zip Borevitz J. Array Genotyping and Mapping, Arabidopsis Protocols

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

organism: Arabidopsis thaliana

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

tag: Age:~6 weeks Tissue:Leaves


title: Ler 2


title: Appressorium induced by cAMP Replicate 4

city: Raleigh

first: Yeon Yee

last: Oh

state: NC

address: NCSU Campus Box 7251

department: Plant Pathology

institute: NCSU

description: Biological replicate 1 of 4. Control germinating cells, untreated, harvested after several passages.

hyb_protocol: The 4 chips were hybridized with their labeled targets for 17 h at 60 °C in the dark. After hybridization, slides were washed sequential according to Agilent Technologies protocol

scan_protocol: Scanned on an Agilent G256BA microarray scanner Images were quantified using Agilent Feature Extraction Software (version 1.6.1.1)

data_processing: LOWESS normalization

organism: Pyricularia grisea

source_name: 50mM cAMP treated; Conidia with appressoria

label_protocol: 1ug of total RNA was labelled by reverse transcriptional incorporation of cyanine 3 (Cy3) or cyanine 5 (Cy5) labelled dCTP, using an oligo(dT) primer. The Agilent Fluorescent Linear Amplification Kit protocol for fluorescent cRNA synthesis (Agilent Technologies) was used.

growth_protocol: RNA from spore germinated on hydrophilic surface of Gelbond for 9 hours,  labeled with Cyanine-3 (green).

extract_protocol: Total RNA extracted using RNAeasy Plant Mini Kit (Qiagen Inc., Valencia, CA) following manufacturer's instructions

tag: 50mM cAMP treated

tag: Conidia with appressoria

source_name: Mock treated; Conidia without appressoria

growth_protocol: RNA from spore germinated on hydrophilic surface of Gelbond for 9 hours, labeled with Cyanine-5 (red).

tag: Mock treated

tag: Conidia without appressoria


title: Peripheral blood_female_Pitta_rep1_Ex.set1&3

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first biological replicate of Pitta females

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

tag: total RNA from peripheral blood cells of first set of pitta prakriti females of age group 18-40yrs labeled with Cy3, and compared with values obtained in set 3


title: Ler 3


title: Appressorium induced by cAMP Replicate 3

growth_protocol: RNA from spore germinated on hydrophilic surface of Gelbond for 9 hours,  labeled with Cyanine-5 (red).

growth_protocol: RNA from spore germinated on hydrophilic surface of Gelbond for 9 hours, labeled with Cyanine-3 (green).


title: Appressorium induced by cAMP Replicate 1


title: fetalliver-Rad23a-DRB

city: Rotterdam

first: Wouter

last: de Laat

address: Dr. Molewaterplein 50

department: Cell Biology

institute: Erasmus MC

description: Unprocessed (not normalized) hybridisation signals were used for analysis. These signals showed clusters of 20-50 positive 4C-signals along the chromosome template. To define the clusters, a running mean or running median was applied, using a window size of 29 probes (on average 60 kb). Obtained values were compared to the running mean/median performed across randomised data. This was done for each array separately. Consequently, all measurements were appreciated relative to the amplitude and noise of that specific array. The False Discovery Rate (FDR), defined as (no. false positives) / (no. of false positives + no. of true positives), was determined as follows: (number of positives in the randomised set) / (number of positives in the data). The threshold level was determined using a top down approach to establish the minimal value for which: FDR<0.05.

hyb_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html

source_name: 4C sample obtained from cultured 14.5 dpc fetal liver cells, digested with HindIII and Sau3A

extract_protocol: 4C was performed as described before in Simonis et al. 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 38(11):1348-54

treatment_protocol: The cultured fetal liver cells were treated for 3 hours with 100 micromolar DRB.

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing the murine Rad23a gene.


title: Col-0-1


title: Col-0-2


title: Col-0 3